From d708ee188587d3d4c533b7dd88124373055c3f38 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Tue, 9 Jul 2024 15:06:59 +0200 Subject: [PATCH] patch modules --- modules.json | 291 +++++++++++++-------------------------------------- 1 file changed, 73 insertions(+), 218 deletions(-) diff --git a/modules.json b/modules.json index 65db947..9aa3063 100644 --- a/modules.json +++ b/modules.json @@ -8,507 +8,366 @@ "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/consensus": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "a3893076a76e91b3ff152faddf872f00778fb224", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/mpileup": { "branch": "master", "git_sha": "e7df38a545d7d72083eededabd8849f731a01502", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", "git_sha": "618364f55cb88f6c283f6c6c45c24d5f9f08f998", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/maskfasta": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bedtools/maskfasta/bedtools-maskfasta.diff" }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "blast/blastn": { "branch": "master", "git_sha": "209e5a3e2753c5e628736a662c877c20f341ee15", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "blast/makeblastdb": { "branch": "master", "git_sha": "a01c66c96e0bc610ad126e7adc4a94cd4acd1b48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/align": { "branch": "master", "git_sha": "0fe30831abbc2ed115e46e92330edf38f56edc3d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bracken/bracken": { "branch": "master", "git_sha": "f362bca32735a848feb314d601db1cee584ee0d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "b97197968ac12dde2463fa54541f6350c46f2035", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", "git_sha": "7081e04c18de9480948d34513a1c1e2d0fa9126d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", "git_sha": "3afb95b2e15fc4a2347470255a7ef654f650c8ec", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cdhit/cdhitest": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/cdhit/cdhitest/cdhit-cdhitest.diff" }, "checkv/downloaddatabase": { "branch": "master", "git_sha": "56cf5a89c2646ad50195635cf18df4028a6928ce", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "checkv/endtoend": { "branch": "master", "git_sha": "56cf5a89c2646ad50195635cf18df4028a6928ce", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "emboss/cons": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080", - "installed_by": [ - "fastq_fastqc_umitools_fastp" - ] + "installed_by": ["fastq_fastqc_umitools_fastp"] }, "fastqc": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", - "installed_by": [ - "fastq_fastqc_umitools_fastp" - ] + "installed_by": ["fastq_fastqc_umitools_fastp"] }, "gunzip": { "branch": "master", "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "humid": { "branch": "master", "git_sha": "c4174581360d2bc32c08cd39cb6a1d1c82212ff6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ivar/consensus": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ivar/consensus/ivar-consensus.diff" }, "ivar/variants": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ivar/variants/ivar-variants.diff" }, "kaiju/kaiju": { "branch": "master", "git_sha": "3db50674956b1fb3741a44eb917458d788a50197", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kaiju/kaiju2krona": { "branch": "master", "git_sha": "3db50674956b1fb3741a44eb917458d788a50197", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kaiju/kaiju2table": { "branch": "master", "git_sha": "3db50674956b1fb3741a44eb917458d788a50197", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/kaiju/kaiju2table/kaiju-kaiju2table.diff" }, "kraken2/kraken2": { "branch": "master", "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff" }, "krakentools/kreport2krona": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "krona/ktimporttext": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mafft": { "branch": "master", "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mash/dist": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mash/dist/mash-dist.diff" }, "mash/screen": { "branch": "master", "git_sha": "10f1f6526942539d5368cedb05afd1aa16eda5be", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mash/sketch": { "branch": "master", "git_sha": "10f1f6526942539d5368cedb05afd1aa16eda5be", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "megahit": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/megahit/megahit.diff" }, "minimap2/align": { "branch": "master", "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/index": { "branch": "master", "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mmseqs/cluster": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mmseqs/createdb": { "branch": "master", "git_sha": "18a43d316b6fd683dc2346867b42882b99811cfd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mmseqs/createtsv": { "branch": "master", "git_sha": "5d849d54f06174c3313eb50c776d4916912db16b", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mmseqs/createtsv/mmseqs-createtsv.diff" }, "mmseqs/easysearch": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mmseqs/easysearch/mmseqs-easysearch.diff" }, "mmseqs/linclust": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/multiqc/multiqc.diff" }, "muscle": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "quast": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/quast/quast.diff" }, "samtools/faidx": { "branch": "master", "git_sha": "f153f1f10e1083c49935565844cccb7453021682", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools", - "modules" - ] + "installed_by": ["bam_stats_samtools", "modules"] }, "seqkit/replace": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimmomatic": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trinity": { "branch": "master", "git_sha": "e06c5f45395d6e34531257b125d410a298a3bd4f", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/trinity/trinity.diff" }, "umitools/dedup": { "branch": "master", "git_sha": "3bd4f34e3093c2a16e6a8eefc22242b9b94641db", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "umitools/extract": { "branch": "master", "git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744", - "installed_by": [ - "fastq_fastqc_umitools_fastp" - ] + "installed_by": ["fastq_fastqc_umitools_fastp"] }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vrhyme/vrhyme": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/vrhyme/vrhyme/vrhyme-vrhyme.diff" }, "vsearch/cluster": { "branch": "master", "git_sha": "d97b335eb448073c1b680710303c02a55f40c77c", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/vsearch/cluster/vsearch-cluster.diff" } } @@ -518,19 +377,15 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_fastqc_umitools_fastp": { "branch": "master", "git_sha": "e98edb838fb0072c0783139ed16723bbc5d48d23", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +}