Update GATK4_HAPLOTYPECALLER module (#4594)

* add a meta to all input files

* update tests to include extra metas

* update meta.yml

* add nf-tests

* migrate to nf-tests

* remove old pytest

* Informative names to metas. fix example metas in meta.yml

* assert versions.yml md5sum

* rename metas

* unique names for snapshots

modules/nf-core/gatk4/haplotypecaller/meta.yml

@@ -39,7 +39,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - fasta:
       type: file
       description: The reference fasta file
@@ -48,7 +48,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - fai:
       type: file
       description: Index of reference fasta file
@@ -57,7 +57,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - dict:
       type: file
       description: GATK sequence dictionary
@@ -66,15 +66,15 @@ input:
       type: map
       description: |
         Groovy Map containing dbsnp information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp:
       type: file
       description: VCF file containing known sites (optional)
   - meta6:
       type: map
       description: |
         Groovy Map containing dbsnp information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp_tbi:
       type: file
       description: VCF index of dbsnp (optional)

modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test

@@ -36,9 +36,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_bam_input") },
             )
         }
 
@@ -69,9 +69,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_input") },
             )
         }
 
@@ -102,9 +102,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_input_with_sites") },
             )
         }
 
@@ -135,9 +135,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_dragstr_input_with_sites") },
             )
         }