diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 0b7d16b2fa2..de4acc421af 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_AMPLICONCLIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap index 6706f947bf7..036c875d040 100644 --- a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap @@ -1,29 +1,17 @@ { - "bam_bed_versions": { - "content": [ - [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-28T15:43:25.843761003" - }, - "bam_bed_stats": { + "bam_bed_save_all_versions": { "content": [ [ - + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-02T13:43:02.239309" + "timestamp": "2024-09-16T07:45:31.382344883" }, - "bam_bed_save_all_stats": { + "bam_bed_save_all_rejects_bam": { "content": [ [ [ @@ -31,45 +19,27 @@ "id": "test", "single_end": false }, - "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a" + "test.cliprejects.bam:md5,8aa0f82e1c2dbfd9fcfab0fe3efa0ada" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-02T13:43:14.110481" + "timestamp": "2024-09-16T07:45:31.334527155" }, - "bam_bed_save_all_versions": { + "bam_bed_versions": { "content": [ [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:36.405710677" - }, - "bam_bed_save_all_rejects_bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.cliprejects.bam:md5,e3c76daf46d83b2327a1168170b08fca" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-28T15:43:36.39935122" + "timestamp": "2024-09-16T07:45:11.300085385" }, "bam_bed_save_clipsats_name": { "content": [ @@ -99,15 +69,27 @@ "id": "test", "single_end": false }, - "test.cliprejects.bam:md5,f29869fea697a5041f588970d9cf2392" + "test.cliprejects.bam:md5,9d0caf53bd9a8ccb4a5ce60393635ee0" ] ] ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:45:21.573836864" + }, + "bam_bed_stats": { + "content": [ + [ + + ] + ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" }, - "timestamp": "2024-05-28T15:43:31.133760457" + "timestamp": "2024-02-02T13:43:02.239309" }, "bam_bed_save_clipsats_stats": { "content": [ @@ -121,17 +103,35 @@ }, "timestamp": "2024-02-13T16:13:25.207756781" }, - "bam_bed_save_clipsats_versions": { + "bam_bed_save_all_stats": { "content": [ [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" + [ + { + "id": "test", + "single_end": false + }, + "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T13:43:14.110481" + }, + "bam_bed_save_clipsats_versions": { + "content": [ + [ + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:31.138774495" + "timestamp": "2024-09-16T07:45:21.620404522" }, "bam_bed_save_all_name": { "content": [ diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index a34a13a9848..1d3049e565d 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap index aa0f8c34d10..17ea1d4f904 100644 --- a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap @@ -51,25 +51,25 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,90c1cf8971540ef05e330db5a560195c" + "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:52.415053401" + "timestamp": "2024-09-16T07:46:07.695175929" }, "bam_split_versions": { "content": [ [ - "versions.yml:md5,90c1cf8971540ef05e330db5a560195c" + "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:57.740193087" + "timestamp": "2024-09-16T07:46:17.91793415" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/calmd/main.nf b/modules/nf-core/samtools/calmd/main.nf index 4672af6f002..fba8aa70e64 100644 --- a/modules/nf-core/samtools/calmd/main.nf +++ b/modules/nf-core/samtools/calmd/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CALMD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/calmd/tests/main.nf.test.snap b/modules/nf-core/samtools/calmd/tests/main.nf.test.snap index fd40d084fa2..4438609f97d 100644 --- a/modules/nf-core/samtools/calmd/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/calmd/tests/main.nf.test.snap @@ -22,25 +22,25 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd" + "versions.yml:md5,6082f9d3311ea0138839acc5341c115f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:47.344537089" + "timestamp": "2024-09-16T07:47:04.212973938" }, "bam_versions": { "content": [ [ - "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd" + "versions.yml:md5,6082f9d3311ea0138839acc5341c115f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:41.963108136" + "timestamp": "2024-09-16T07:46:53.00613089" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/cat/main.nf b/modules/nf-core/samtools/cat/main.nf index 9447b657220..0490b81d3f5 100644 --- a/modules/nf-core/samtools/cat/main.nf +++ b/modules/nf-core/samtools/cat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") @@ -26,7 +26,6 @@ process SAMTOOLS_CAT { """ samtools \\ cat \\ - --threads ${task.cpus-1} \\ $args \\ -o ${prefix}.${file_type} \\ $input_files diff --git a/modules/nf-core/samtools/cat/tests/main.nf.test.snap b/modules/nf-core/samtools/cat/tests/main.nf.test.snap index ae9344df6f0..9af1b19ff9e 100644 --- a/modules/nf-core/samtools/cat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/cat/tests/main.nf.test.snap @@ -14,14 +14,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8" + "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:35.044644556" + "timestamp": "2024-09-16T07:47:51.511914861" }, "bams_bam": { "content": [ @@ -58,13 +58,13 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8" + "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:29.652817652" + "timestamp": "2024-09-16T08:47:50.783194958" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 748fc4020d0..a0d831ff278 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COLLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test.snap b/modules/nf-core/samtools/collate/tests/main.nf.test.snap index 8645f3b69df..4d2213695a7 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collate/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "cram_fasta_versions": { "content": [ [ - "versions.yml:md5,b88681026fe2f488e3704e6726464d26" + "versions.yml:md5,354d4c20293fa674e56f96d5f7db6580" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:11.322474854" + "timestamp": "2024-09-16T07:48:41.845649492" }, "bam_cram": { "content": [ @@ -82,13 +82,13 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,b88681026fe2f488e3704e6726464d26" + "versions.yml:md5,354d4c20293fa674e56f96d5f7db6580" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:04.384976938" + "timestamp": "2024-09-16T07:48:29.622364238" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 599c1b78ab0..8b70ebd3452 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COLLATEFASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap b/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap index 3618619eadd..26f5293699c 100644 --- a/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap @@ -17,14 +17,14 @@ ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-27T08:53:29.440496728" + "timestamp": "2024-09-16T07:50:35.483719031" }, "human - bam - single_end": { "content": [ @@ -38,14 +38,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T13:36:44.978865568" + "timestamp": "2024-09-16T07:49:31.667042764" }, "human - bam - paired_end -stub": { "content": [ @@ -62,14 +62,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:12:21.528678233" + "timestamp": "2024-09-16T07:50:04.607920717" }, "human - cram - stub": { "content": [ @@ -86,14 +86,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:13:01.876034822" + "timestamp": "2024-09-16T07:50:25.354607106" }, "human - cram": { "content": [ @@ -110,14 +110,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T09:23:07.374415578" + "timestamp": "2024-09-16T07:49:43.12646213" }, "human - bam - paired_end - interleaved": { "content": [ @@ -137,14 +137,14 @@ ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T12:02:17.198640965" + "timestamp": "2024-09-16T07:49:53.799565712" }, "human - bam - single_end - stub": { "content": [ @@ -158,14 +158,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:12:39.204428667" + "timestamp": "2024-09-16T07:50:15.487972669" }, "human - bam - paired_end": { "content": [ @@ -182,13 +182,13 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T13:31:43.988112588" + "timestamp": "2024-09-16T07:49:19.805942524" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index 5a85438e08a..699c05ce8b6 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::samtools=1.20" + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/consensus/main.nf b/modules/nf-core/samtools/consensus/main.nf index 3339580682b..6f66c5ae409 100644 --- a/modules/nf-core/samtools/consensus/main.nf +++ b/modules/nf-core/samtools/consensus/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONSENSUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_1': - 'biocontainers/samtools:1.20--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -37,7 +37,7 @@ process SAMTOOLS_CONSENSUS { cat <<-END_VERSIONS > versions.yml "${task.process}": - samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -54,7 +54,7 @@ process SAMTOOLS_CONSENSUS { cat <<-END_VERSIONS > versions.yml "${task.process}": - samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test b/modules/nf-core/samtools/consensus/tests/main.nf.test index bf321106a8d..85163731d56 100644 --- a/modules/nf-core/samtools/consensus/tests/main.nf.test +++ b/modules/nf-core/samtools/consensus/tests/main.nf.test @@ -16,8 +16,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ]) """ } @@ -39,9 +38,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) """ } } @@ -62,9 +59,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ]) """ } } @@ -87,9 +82,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) """ } } diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test.snap b/modules/nf-core/samtools/consensus/tests/main.nf.test.snap index afdc8617e8d..6afeb5c3fe9 100644 --- a/modules/nf-core/samtools/consensus/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/consensus/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:50.610585" + "timestamp": "2024-09-17T09:30:20.800066273" }, "sarscov2 - bam - stub": { "content": [ @@ -65,7 +65,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:54.651067" + "timestamp": "2024-09-17T09:30:38.211253068" }, "sarscov2 - bam - fasta": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -130,15 +130,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:42.303778" + "timestamp": "2024-09-17T09:29:47.601535754" }, "sarscov2 - bam - fastq": { "content": [ @@ -159,7 +159,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -177,14 +177,14 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:46.516552" + "timestamp": "2024-09-17T09:30:06.666785126" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 03b7b5259db..cf9253d10f2 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 513629022bd..a021254e8ba 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -22,26 +22,26 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:34.618037105" + "timestamp": "2024-09-16T07:52:35.516411351" }, "bam_to_cram_versions": { "content": [ [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:29.165839679" + "timestamp": "2024-09-16T07:52:24.694454205" }, "stub": { "content": [ @@ -71,7 +71,7 @@ ] ], "4": [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ], "bai": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:40.258233921" + "timestamp": "2024-09-16T07:52:45.799885099" }, "bam_to_cram_index": { "content": [ diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf index af8438eafd6..e386132fd84 100644 --- a/modules/nf-core/samtools/coverage/main.nf +++ b/modules/nf-core/samtools/coverage/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COVERAGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap index 63e260514b4..b9ddb18df5a 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:47.4359515" + "timestamp": "2024-09-16T07:53:42.773351407" }, "test_samtools_coverage_bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:36.39684853" + "timestamp": "2024-09-16T07:53:22.798338025" }, "test_samtools_coverage_cram": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -94,14 +94,14 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:42.036690983" + "timestamp": "2024-09-16T07:53:32.409876082" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/cramsize/environment.yml b/modules/nf-core/samtools/cramsize/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/cramsize/environment.yml +++ b/modules/nf-core/samtools/cramsize/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/cramsize/main.nf b/modules/nf-core/samtools/cramsize/main.nf index c5ba5e03723..1e1b378aef3 100644 --- a/modules/nf-core/samtools/cramsize/main.nf +++ b/modules/nf-core/samtools/cramsize/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CRAMSIZE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(cram) diff --git a/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap b/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap index 834fe42484a..39aa62365a2 100644 --- a/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ], "size": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-03T13:38:57.726189593" + "timestamp": "2024-09-16T07:54:30.618612676" }, "human - cram": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ], "size": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-03T13:38:46.273448099" + "timestamp": "2024-09-16T07:54:20.179335064" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index c6fc529f786..3af598d6c23 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_DEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta1), path(bam) diff --git a/modules/nf-core/samtools/depth/tests/main.nf.test.snap b/modules/nf-core/samtools/depth/tests/main.nf.test.snap index eea108d3351..f5523cbf765 100644 --- a/modules/nf-core/samtools/depth/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/depth/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ], "tsv": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:57:20.065271" + "timestamp": "2024-09-16T07:55:28.207892316" }, "test-samtools-depth": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ], "tsv": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:57:13.724175" + "timestamp": "2024-09-16T07:55:17.233534429" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 52be415f0b7..707a72e4837 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_DICT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/dict/tests/main.nf.test.snap b/modules/nf-core/samtools/dict/tests/main.nf.test.snap index 66d7b1fcff5..ca039e7cd8a 100644 --- a/modules/nf-core/samtools/dict/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/dict/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d" + "versions.yml:md5,6903afebec7d19e8beeb0f903a782a2c" ], "dict": [ [ @@ -24,27 +24,27 @@ ] ], "versions": [ - "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d" + "versions.yml:md5,6903afebec7d19e8beeb0f903a782a2c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T09:43:30.509703257" + "timestamp": "2024-09-16T07:57:07.279372555" }, "sarscov2 - fasta": { "content": [ "@HD\tVN:1.0\tSO:unsorted", [ - "versions.yml:md5,0af6b2d2d6d9d96bc5abe98b99b91446" + "versions.yml:md5,f6b1fc0172793465c9e43110de9f3a4f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-30T12:12:31.201483952" + "timestamp": "2024-09-16T07:56:55.930509023" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index bdcdbc954df..28c0a81cf79 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3223b72bc6e..1bbb3ec2b07 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:14.779784761" + "timestamp": "2024-09-16T07:57:47.450887871" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:20.256633877" + "timestamp": "2024-09-16T07:58:04.804905659" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -142,15 +142,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:25.632577273" + "timestamp": "2024-09-16T07:58:23.831268154" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -189,15 +189,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:31.058424849" + "timestamp": "2024-09-16T07:58:35.600243706" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -236,14 +236,14 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:36.479929617" + "timestamp": "2024-09-16T07:58:54.705460167" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 056f2f4ec91..1c42141a3dc 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fasta/tests/main.nf.test.snap b/modules/nf-core/samtools/fasta/tests/main.nf.test.snap index 36cdb60e8cd..6c26c7e8b4f 100644 --- a/modules/nf-core/samtools/fasta/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fasta/tests/main.nf.test.snap @@ -8,27 +8,27 @@ "test_singleton.fasta.gz", "test_other.fasta.gz", [ - "versions.yml:md5,169b03a7e4a82c620276542932c1312d" + "versions.yml:md5,da649728a4a937a64cb8865ebc9ace81" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:51:59.909648" + "timestamp": "2024-09-16T07:59:47.290462747" }, "test-samtools-fasta-interleave": { "content": [ ">ERR5069949.2151832/1", "test_other.fasta.gz", [ - "versions.yml:md5,169b03a7e4a82c620276542932c1312d" + "versions.yml:md5,da649728a4a937a64cb8865ebc9ace81" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:52:04.127593" + "timestamp": "2024-09-16T07:59:59.597655297" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 6796c02b682..136744d5aad 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap index 1ba09d3a3ba..10e5cd3d77f 100644 --- a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap @@ -93,26 +93,26 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:40.362380302" + "timestamp": "2024-09-16T08:00:41.44921616" }, "bam_verinterleave_sions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:45.632731997" + "timestamp": "2024-09-16T08:00:56.47781168" }, "bam_singleton": { "content": [ diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 6d29ae2da74..c8169fcba54 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FIXMATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap b/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap index e9507d5d054..a178a78ca76 100644 --- a/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,57175fc36f563ce7907bc6d1c0dd1625" + "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:45.339827663" + "timestamp": "2024-09-16T08:01:53.33860034" }, "bam": { "content": [ diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 754d84b73fc..4a49972747d 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c61209..04c3852b26c 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:28.002887" + "timestamp": "2024-09-16T08:02:58.866491759" }, "BAM": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:13.330971" + "timestamp": "2024-09-16T08:02:47.383332837" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 8f41ad3d4ac..fdd29470543 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_GETRG { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/getrg/tests/main.nf.test.snap b/modules/nf-core/samtools/getrg/tests/main.nf.test.snap index 338d5e7711f..36e1130f7c5 100644 --- a/modules/nf-core/samtools/getrg/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/getrg/tests/main.nf.test.snap @@ -5,13 +5,13 @@ "@RG\tID:1\tLB:lib1\tPL:ILLUMINA\tSM:test\tPU:barcode1" ], [ - "versions.yml:md5,b2f2aff0694b71ae5d2225d85bbfba9d" + "versions.yml:md5,40cf98b3daaf262b18e889ea734dbc40" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:28:18.826853" + "timestamp": "2024-09-16T08:11:06.35329516" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2ea2a5ccded..c4b5a0a3f53 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104e68..2cc89a3b833 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:56.180093" + "timestamp": "2024-09-16T08:11:56.466856235" }, "bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:41.408704" + "timestamp": "2024-09-16T08:11:46.311550359" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/import/main.nf b/modules/nf-core/samtools/import/main.nf index 954a8052003..e0a51c03371 100644 --- a/modules/nf-core/samtools/import/main.nf +++ b/modules/nf-core/samtools/import/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b9ea..311756102d3 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199cea7..72d65e81af3 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:53.9057" + "timestamp": "2024-09-16T08:21:25.261127166" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-09-16T08:21:12.653194876" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-09-16T08:21:01.854932651" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-09-16T08:20:51.485364222" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-09-16T08:20:40.518873972" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 9129c55b2f5..8453bf82bae 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MARKDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/tests/main.nf.test b/modules/nf-core/samtools/markdup/tests/main.nf.test new file mode 100644 index 00000000000..acfbd1c166e --- /dev/null +++ b/modules/nf-core/samtools/markdup/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process SAMTOOLS_MARKDUP" + script "../main.nf" + process "SAMTOOLS_MARKDUP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/fixmate" + tag "samtools/sort" + tag "samtools/markdup" + + test("sarscov2 - bam") { + setup { + run("SAMTOOLS_FIXMATE") { + script "../../fixmate/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + ] + """ + } + } + run("SAMTOOLS_SORT") { + script "../../sort/main.nf" + process { + """ + input[0] = SAMTOOLS_FIXMATE.out.bam + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + } + when { + process { + """ + input[0] = SAMTOOLS_SORT.out.bam + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/markdup/tests/main.nf.test.snap b/modules/nf-core/samtools/markdup/tests/main.nf.test.snap new file mode 100644 index 00000000000..4e7cbf5ead5 --- /dev/null +++ b/modules/nf-core/samtools/markdup/tests/main.nf.test.snap @@ -0,0 +1,96 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:46:57.510270753" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,e73ea77e3857e7c6b0e6db2ec660361f" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,e73ea77e3857e7c6b0e6db2ec660361f" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:51:17.068686604" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/markdup/nextflow.config b/modules/nf-core/samtools/markdup/tests/nextflow.config similarity index 60% rename from tests/modules/nf-core/samtools/markdup/nextflow.config rename to modules/nf-core/samtools/markdup/tests/nextflow.config index 0d7fb4f5597..1a2b52b9888 100644 --- a/tests/modules/nf-core/samtools/markdup/nextflow.config +++ b/modules/nf-core/samtools/markdup/tests/nextflow.config @@ -1,24 +1,14 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: SAMTOOLS_COLLATE { ext.prefix = { "${meta.id}.collate" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_FIXMATE { ext.prefix = { "${meta.id}.fixmate" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_SORT { ext.prefix = { "${meta.id}.sorted" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_MARKDUP { ext.prefix = { "${meta.id}.markdup" } } - } diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 693b1d80f40..34da4c7c870 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 17bc846fa28..0a41e01af63 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:35.851936597" + "timestamp": "2024-09-16T09:16:30.476887194" }, "bams_csi": { "content": [ @@ -124,14 +124,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:41.405707643" + "timestamp": "2024-09-16T09:16:52.203823961" }, "bam_cram": { "content": [ @@ -158,14 +158,14 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:51.695689923" + "timestamp": "2024-09-16T08:29:57.524363148" }, "crams_bam": { "content": [ @@ -182,14 +182,14 @@ "crams_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:30.185392319" + "timestamp": "2024-09-16T09:16:06.977096207" }, "bam_csi": { "content": [ diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index b51f96d369a..a45c6045b19 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MPILEUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap index 76b2086b40b..fb6b6f1b7d0 100644 --- a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap @@ -2,26 +2,26 @@ "bam_bed_versions": { "content": [ [ - "versions.yml:md5,449485eab74a465dc9023760be2c12a1" + "versions.yml:md5,0ad5d578348ec8f358197302530db925" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:41.535946155" + "timestamp": "2024-09-16T09:20:04.969588285" }, "bam_bed_fasta_versions": { "content": [ [ - "versions.yml:md5,449485eab74a465dc9023760be2c12a1" + "versions.yml:md5,0ad5d578348ec8f358197302530db925" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:46.787790118" + "timestamp": "2024-09-16T09:20:30.887599345" }, "bam_bed_mpileup": { "content": [ diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/reheader/main.nf b/modules/nf-core/samtools/reheader/main.nf index 2ffe8de2be8..063854206f2 100644 --- a/modules/nf-core/samtools/reheader/main.nf +++ b/modules/nf-core/samtools/reheader/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) @@ -41,7 +41,7 @@ process SAMTOOLS_REHEADER { """ touch ${prefix}.bam - ccat <<-END_VERSIONS > versions.yml + cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS diff --git a/modules/nf-core/samtools/reheader/tests/chrdel.config b/modules/nf-core/samtools/reheader/tests/chrdel.config new file mode 100644 index 00000000000..7b5da49a40b --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/chrdel.config @@ -0,0 +1,6 @@ +process { + withName: SAMTOOLS_REHEADER { + ext.args = "--command 'sed -E \"s/^(@SQ.*)(\\tSN:)chr/\\1\\2/\"'" + ext.prefix = { "${meta.id}_chrDel" } + } +} diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test b/modules/nf-core/samtools/reheader/tests/main.nf.test new file mode 100644 index 00000000000..53142525d15 --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process SAMTOOLS_REHEADER" + script "../main.nf" + process "SAMTOOLS_REHEADER" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/reheader" + + test("homo_sapiens - chrdel") { + config "./chrdel.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - rgdel") { + config "./rgdel.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test.snap b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap new file mode 100644 index 00000000000..885ee35041b --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "homo_sapiens - chrdel": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_chrDel.bam:md5,957d2d542fb9bbd6511df9c0b5069ce4" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test_chrDel.bam:md5,957d2d542fb9bbd6511df9c0b5069ce4" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:28:17.577422205" + }, + "homo_sapiens - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:26:34.99215454" + }, + "homo_sapiens - rgdel": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_rgDel.bam:md5,02e7512a76fd9df1905ee90558365b0c" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test_rgDel.bam:md5,02e7512a76fd9df1905ee90558365b0c" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:23:30.403448169" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/reheader/tests/rgdel.config b/modules/nf-core/samtools/reheader/tests/rgdel.config new file mode 100644 index 00000000000..03a2dc8554f --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/rgdel.config @@ -0,0 +1,6 @@ +process { + withName: SAMTOOLS_REHEADER { + ext.args = "--command 'grep -v ^@RG'" + ext.prefix = { "${meta.id}_rgDel" } + } +} diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/sormadup/main.nf b/modules/nf-core/samtools/sormadup/main.nf index 9b39fd9532a..e8ac9b1c7ee 100644 --- a/modules/nf-core/samtools/sormadup/main.nf +++ b/modules/nf-core/samtools/sormadup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORMADUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -37,7 +37,6 @@ process SAMTOOLS_SORMADUP { """ samtools cat \\ - --threads $task.cpus \\ $args \\ ${input} \\ | \\ diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap index c4a5a6399cb..0a38f7f0c37 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap @@ -30,7 +30,7 @@ ] ], "5": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ], "bam": [ [ @@ -60,15 +60,15 @@ ] ], "versions": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:23.721871158" + "timestamp": "2024-09-16T08:56:24.200237922" }, "sarscov2 - bam": { "content": [ @@ -79,7 +79,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,810247d7c843e3cb54872d97ed9df4a9" + "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" ] ], "1": [ @@ -101,7 +101,7 @@ ] ], "5": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ], "bam": [ [ @@ -109,7 +109,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,810247d7c843e3cb54872d97ed9df4a9" + "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" ] ], "crai": [ @@ -131,14 +131,14 @@ ] ], "versions": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:18.300807204" + "timestamp": "2024-09-16T08:56:12.101922642" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099c0f..acfd9252ce4 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d15c5..2d6b2900432 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-09-16T08:49:58.207549273" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ] ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -84,15 +84,15 @@ ] ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-09-16T08:50:08.630951018" }, "cram - stub": { "content": [ @@ -122,7 +122,7 @@ ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ @@ -149,15 +149,15 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" }, "bam": { "content": [ @@ -167,7 +167,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +180,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-09-16T08:49:43.971158333" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 982bc28e7fb..493525a9e0e 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f37880a..df507be7a36 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:24.885816" + "timestamp": "2024-09-16T09:29:16.767396182" }, "bam - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:39.310713" + "timestamp": "2024-09-16T09:29:29.721580274" }, "cram - stub": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:21:04.771199" + "timestamp": "2024-09-16T09:29:53.567964304" }, "bam": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -125,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:19:06.645466" + "timestamp": "2024-09-16T09:28:50.73610604" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index da2df5e43a4..09ad4c10750 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index dc611448c3d..37e05cec887 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6bcce9fea70..29e7aeb08eb 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -56,14 +56,14 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:20.390692583" + "timestamp": "2024-09-16T09:26:24.461775464" }, "cram_to_bam_index_cram": { "content": [ @@ -169,6 +169,16 @@ }, "timestamp": "2024-02-12T19:37:56.490286" }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_csi": { "content": [ [ @@ -208,14 +218,14 @@ "cram_to_bam_index_qname_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:15.007493874" + "timestamp": "2024-09-16T09:25:51.953436682" }, "cram_to_bam_bam": { "content": [ @@ -240,14 +250,14 @@ "cram_to_bam_index_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:09.472376824" + "timestamp": "2024-09-16T09:25:14.475388399" }, "cram_to_bam_bai": { "content": [ @@ -264,14 +274,14 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:04.080050906" + "timestamp": "2024-09-16T09:24:49.673441798" }, "cram_bam": { "content": [ @@ -355,37 +365,17 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, - "cram_to_bam_index_qname_unselected": { - "content": [ - "test.unselected.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.322874" - }, - "cram_to_bam_index_qname_unselected_csi": { - "content": [ - "test.unselected.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.328458" - }, "bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:52.978954857" + "timestamp": "2024-09-16T09:23:27.151650338" }, "cram_to_bam_index_qname_cram": { "content": [ @@ -450,14 +440,24 @@ "cram_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:24:12.95416913" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" }, - "timestamp": "2024-05-28T15:42:58.400776109" + "timestamp": "2024-02-12T19:38:23.322874" }, "bam_sam": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap index e0c32a77e3a..ccb96576367 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap @@ -7,15 +7,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,34e1f13bd6e6b78bb8a589560222e343" + "test.stats:md5,498621f92e86d55e4f7ae93170e6e733" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T07:42:00.089356713" + "timestamp": "2024-09-16T08:04:02.179870196" }, "test_bam_dedup_stats_samtools_umicollapse_flagstats": { "content": [ @@ -47,18 +47,18 @@ ] ], [ - "versions.yml:md5,15f852de3d9e3fb11c786d15873c5d16", + "versions.yml:md5,20605eb79c410c0ed179ba660d82f75b", + "versions.yml:md5,23617661d2c899996bee2b05db027e25", "versions.yml:md5,268e43f34038d4c6146ed050630f95b4", - "versions.yml:md5,543112ba38e0fae7ae41be77cf1e0791", - "versions.yml:md5,7f6271d4e25dc8c739f28a15399787db", - "versions.yml:md5,d241a309a3e0eecfe1d3fe6efa65515c" + "versions.yml:md5,e02a62a393a833778e16542eeed0d148", + "versions.yml:md5,ef00762e264b99ac45713dc0dedf4060" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T07:42:00.053427512" + "timestamp": "2024-09-16T08:04:02.126366857" }, "test_bam_dedup_stats_samtools_umicollapse_idxstats": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 4fd70b5f326..d39f9129b9a 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "test" }, - "test.stats:md5,09d1bd8f10e000921202f7ea1cd0679e" + "test.stats:md5,84891a894010aeb882c4092db9248d2c" ] ], [ @@ -26,18 +26,18 @@ ] ], [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T11:53:11.53709" + "timestamp": "2024-09-16T08:04:23.444693448" }, "sarscov2_bam_bai - stub": { "content": [ @@ -67,7 +67,7 @@ ] ], "3": [ - + ], "4": [ [ @@ -94,10 +94,10 @@ ] ], "7": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ], "bai": [ @@ -117,7 +117,7 @@ ] ], "csi": [ - + ], "deduplog": [ [ @@ -152,18 +152,18 @@ ] ], "versions": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] } ], "meta": { "nf-test": "0.9.0", - 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"versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -137,17 +137,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:57.708621" + "timestamp": "2024-09-16T08:08:24.220305512" }, "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ @@ -180,9 +180,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -212,17 +212,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:20:17.051493" + "timestamp": "2024-09-16T08:08:54.206770141" }, "test_bam_stats_samtools_single_end": { "content": [ @@ -250,20 +250,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,4a0c429c661d6aa0b60acb9309da642d" + "test.stats:md5,291bb2393ec947140d12d42c2795b222" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:25.801394" + "timestamp": "2024-09-16T08:07:49.731645858" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +291,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,7afd486ad6abb9a2a3dac90c99e1d87b" + "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:36.158768" + "timestamp": "2024-09-16T08:08:01.421996172" }, "test_bam_stats_samtools_paired_end_cram": { "content": [ @@ -332,19 +332,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,16b59a1f2c99d9fe30f711adc3ebe32d" + "test.stats:md5,1622856127bafd6cdbadee9cd64ec9b7" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:46.625907" + "timestamp": "2024-09-16T08:08:12.640915756" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap index 8ff1e9c5187..2c6d8787ba1 100644 --- a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "subsample_fraction": 0.06201800538763442, "depth": 2 }, - "NA12878.bam:md5,c998482010b83365a4889c3fa75ac578", + "NA12878.bam:md5,f9f41668c064cb54051f77a18bd6a258", "NA12878.bam.csi:md5,0b4abd161cdcc2b51571c9cc651df354" ], [ @@ -18,7 +18,7 @@ "subsample_fraction": 0.12403601077526884, "depth": 4 }, - "NA12878.bam:md5,d6045df32f7c77d5c863b2068739faa9", + "NA12878.bam:md5,766247cca7d1ccff1352ecc3d47fe4be", "NA12878.bam.csi:md5,3f8f9a17463b6c2391c632681d3f253a" ], [ @@ -27,7 +27,7 @@ "subsample_fraction": 0.062137851766009305, "depth": 2 }, - "NA19401.bam:md5,6b144e7adc1f9e6711aea0e4772c5937", + "NA19401.bam:md5,dd327e50a1d4ba3a8ccaa07a587a2ecf", "NA19401.bam.csi:md5,36c29896003f2de5306ff427a969058c" ], [ @@ -36,14 +36,14 @@ "subsample_fraction": 0.12427570353201861, "depth": 4 }, - "NA19401.bam:md5,3b0d20e5f44952135a547c6230117460", - "NA19401.bam.csi:md5,b44701d7d4de827cc1b83aaeb397deaf" + "NA19401.bam:md5,f678431058d8b4963f09fa3431681756", + "NA19401.bam.csi:md5,14a9e8d58a46360917263c22c07dea41" ] ], "1": [ - "versions.yml:md5,8019e4c6fa3c1ddea25d64d6bfe5651f", + "versions.yml:md5,0b62e253d214b752ae075e2f90d5deaa", "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb", - "versions.yml:md5,f134df55b5047c5a8222ca04cf5ec501" + "versions.yml:md5,fb8f3d6cc806f7d5965e184c4d42fbeb" ], "bam_subsampled": [ [ @@ -52,7 +52,7 @@ "subsample_fraction": 0.06201800538763442, "depth": 2 }, - "NA12878.bam:md5,c998482010b83365a4889c3fa75ac578", + "NA12878.bam:md5,f9f41668c064cb54051f77a18bd6a258", "NA12878.bam.csi:md5,0b4abd161cdcc2b51571c9cc651df354" ], [ @@ -61,7 +61,7 @@ "subsample_fraction": 0.12403601077526884, "depth": 4 }, - "NA12878.bam:md5,d6045df32f7c77d5c863b2068739faa9", + "NA12878.bam:md5,766247cca7d1ccff1352ecc3d47fe4be", "NA12878.bam.csi:md5,3f8f9a17463b6c2391c632681d3f253a" ], [ @@ -70,7 +70,7 @@ "subsample_fraction": 0.062137851766009305, "depth": 2 }, - "NA19401.bam:md5,6b144e7adc1f9e6711aea0e4772c5937", + "NA19401.bam:md5,dd327e50a1d4ba3a8ccaa07a587a2ecf", "NA19401.bam.csi:md5,36c29896003f2de5306ff427a969058c" ], [ @@ -79,14 +79,14 @@ "subsample_fraction": 0.12427570353201861, "depth": 4 }, - "NA19401.bam:md5,3b0d20e5f44952135a547c6230117460", - "NA19401.bam.csi:md5,b44701d7d4de827cc1b83aaeb397deaf" + "NA19401.bam:md5,f678431058d8b4963f09fa3431681756", + "NA19401.bam.csi:md5,14a9e8d58a46360917263c22c07dea41" ] ], "versions": [ - "versions.yml:md5,8019e4c6fa3c1ddea25d64d6bfe5651f", + "versions.yml:md5,0b62e253d214b752ae075e2f90d5deaa", "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb", - "versions.yml:md5,f134df55b5047c5a8222ca04cf5ec501" + "versions.yml:md5,fb8f3d6cc806f7d5965e184c4d42fbeb" ] }, [ @@ -125,9 +125,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-24T11:40:16.846985786" + "timestamp": "2024-09-16T07:55:54.476774933" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap index 408dabff07b..f5a87298236 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap @@ -34,7 +34,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,845655ccfd1fd701b9f692f8db9508af" + "test.stats:md5,0ebab7bf6149e6378b263997d7073067" ] ], [ @@ -47,19 +47,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:06.813423" + "timestamp": "2024-09-16T08:27:35.808393107" }, "sarscov2 - bam - single_end - stub": { "content": [ @@ -134,12 +134,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -211,20 +211,20 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:23.861012" + "timestamp": "2024-09-16T08:10:09.451605417" }, "sarscov2 - bam - paired_end": { "content": [ @@ -261,7 +261,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,603fa8c9e0e9eb3769498fc989a29250" + "test.stats:md5,74b78cbd41df459e1037735f714cda4f" ] ], [ @@ -274,19 +274,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:25.071168" + "timestamp": "2024-09-16T08:28:01.671969576" }, "sarscov2 - bam - paired_end - stub": { "content": [ @@ -361,12 +361,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -438,19 +438,19 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:44.894976" + "timestamp": "2024-09-16T08:10:28.136547114" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 07e2e0108a2..b9c06ca0132 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -587,12 +587,6 @@ rtgtools/format: rtgtools/vcfeval: - modules/nf-core/rtgtools/vcfeval/** - tests/modules/nf-core/rtgtools/vcfeval/** -samtools/markdup: - - modules/nf-core/samtools/markdup/** - - tests/modules/nf-core/samtools/markdup/** -samtools/reheader: - - modules/nf-core/samtools/reheader/** - - tests/modules/nf-core/samtools/reheader/** scramble/clusteranalysis: - modules/nf-core/scramble/clusteranalysis/** - tests/modules/nf-core/scramble/clusteranalysis/** diff --git a/tests/modules/nf-core/samtools/markdup/main.nf b/tests/modules/nf-core/samtools/markdup/main.nf deleted file mode 100644 index 304180a1b4e..00000000000 --- a/tests/modules/nf-core/samtools/markdup/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf' -include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf' -include { SAMTOOLS_SORT } from '../../../../../modules/nf-core/samtools/sort/main.nf' -include { SAMTOOLS_MARKDUP } from '../../../../../modules/nf-core/samtools/markdup/main.nf' - -workflow test_samtools_markdup { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - fasta = [ - [ id:'fasta' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - SAMTOOLS_COLLATE ( input, [[],[]] ) - SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam ) - SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam, fasta ) - SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, fasta ) - -} diff --git a/tests/modules/nf-core/samtools/markdup/test.yml b/tests/modules/nf-core/samtools/markdup/test.yml deleted file mode 100644 index 0a365fa78f5..00000000000 --- a/tests/modules/nf-core/samtools/markdup/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: samtools markdup test_samtools_markdup - command: nextflow run ./tests/modules/nf-core/samtools/markdup -entry test_samtools_markdup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/markdup/nextflow.config - tags: - - samtools/markdup - - samtools - files: - - path: output/samtools/test.markdup.bam - - path: output/samtools/versions.yml diff --git a/tests/modules/nf-core/samtools/reheader/main.nf b/tests/modules/nf-core/samtools/reheader/main.nf deleted file mode 100644 index 1cf6af1f235..00000000000 --- a/tests/modules/nf-core/samtools/reheader/main.nf +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_RGDEL} from '../../../../../modules/nf-core/samtools/reheader/main.nf' -include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_CHRDEL} from '../../../../../modules/nf-core/samtools/reheader/main.nf' - -workflow test_samtools_reheader_chrdel { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - - SAMTOOLS_REHEADER_CHRDEL ( input ) -} - -workflow test_samtools_reheader_rgdel { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - - SAMTOOLS_REHEADER_RGDEL ( input ) -} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/reheader/nextflow.config b/tests/modules/nf-core/samtools/reheader/nextflow.config deleted file mode 100644 index 7a7320f1998..00000000000 --- a/tests/modules/nf-core/samtools/reheader/nextflow.config +++ /dev/null @@ -1,13 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: SAMTOOLS_REHEADER_CHRDEL { - ext.args = "--command 'sed -E \"s/^(@SQ.*)(\\tSN:)chr/\\1\\2/\"'" - ext.prefix = { "${meta.id}_chrDel" } - } - withName: SAMTOOLS_REHEADER_RGDEL { - ext.args = "--command 'grep -v ^@RG'" - ext.prefix = { "${meta.id}_rgDel" } - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/reheader/test.yml b/tests/modules/nf-core/samtools/reheader/test.yml deleted file mode 100644 index b35b79ab484..00000000000 --- a/tests/modules/nf-core/samtools/reheader/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: samtools reheader test_samtools_reheader_chrdel - command: nextflow run ./tests/modules/nf-core/samtools/reheader -entry test_samtools_reheader_chrdel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/reheader/nextflow.config - tags: - - samtools/reheader - - samtools - files: - - path: output/samtools/test_chrDel.bam - - path: output/samtools/versions.yml - -- name: samtools reheader test_samtools_reheader_rgdel - command: nextflow run ./tests/modules/nf-core/samtools/reheader -entry test_samtools_reheader_rgdel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/reheader/nextflow.config - tags: - - samtools/reheader - - samtools - files: - - path: output/samtools/test_rgDel.bam - - path: output/samtools/versions.yml