adding versioning

nf-core · Nov 26, 2024 · b0ce95b · b0ce95b
1 parent 01d82ef
commit b0ce95b
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Showing 4 changed files with 27 additions and 1 deletion.
diff --git a/subworkflows/local/bam_snp_variant_calling/main.nf b/subworkflows/local/bam_snp_variant_calling/main.nf
@@ -13,6 +13,8 @@ workflow BAM_SNP_VARIANT_CALLING {
     intervals
 
     main:
+    ch_versions = Channel.empty()
+
     //deepvariant
     if (params.snv_caller === 'deepvariant') {
         deepvar_input_ch = sorted_bam.join(sorted_bai)
@@ -26,6 +28,7 @@ workflow BAM_SNP_VARIANT_CALLING {
                                     [[], []]
                                     )
         vcf_ch = DEEPVARIANT_RUNDEEPVARIANT.out.vcf.join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf_tbi)
+        ch_versions = ch_versions.mix(DEEPVARIANT_RUNDEEPVARIANT.out.versions)
     }
 
     //gatk4_haplotypecaller
@@ -44,8 +47,11 @@ workflow BAM_SNP_VARIANT_CALLING {
                             )
 
         vcf_ch = GATK4_HAPLOTYPECALLER.out.vcf.join(GATK4_HAPLOTYPECALLER.out.tbi)
+        ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions)
+
     }
 
     emit:
     vcf_ch
+    versions       = ch_versions
 }
diff --git a/subworkflows/local/bam_sv_variant_calling/main.nf b/subworkflows/local/bam_sv_variant_calling/main.nf
@@ -11,6 +11,8 @@ workflow BAM_SV_VARIANT_CALLING {
     fasta_fai
 
     main:
+    ch_versions = Channel.empty()
+
     //call the structural variants
     PBSV_DISCOVER(sorted_bam, fasta)
     PBSV_CALL(PBSV_DISCOVER.out.svsig, fasta)
@@ -21,6 +23,13 @@ workflow BAM_SV_VARIANT_CALLING {
 
     vcf_ch = TABIX_BGZIP.out.output.join(BCFTOOLS_INDEX.out.csi)
 
+    ch_versions = ch_versions.mix(PBSV_DISCOVER.out.versions)
+    ch_versions = ch_versions.mix(PBSV_CALL.out.versions)
+    ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions)
+    ch_versions = ch_versions.mix(BCFTOOLS_INDEX.out.versions)
+
     emit:
     vcf_ch
+    versions       = ch_versions
+
 }
diff --git a/subworkflows/local/repeat_characterization/main.nf b/subworkflows/local/repeat_characterization/main.nf
@@ -15,6 +15,8 @@ workflow  REPEAT_CHARACTERIZATION{
     repeat_id
 
     main:
+    ch_versions = Channel.empty()
+
     bam_bai_ch = sorted_bam.join(sorted_bai)
     //genotype the repeat region
     TRGT_GENOTYPE(bam_bai_ch,
@@ -41,4 +43,14 @@ workflow  REPEAT_CHARACTERIZATION{
                 fasta_fai,
                 bed,
                 repeat_id)
+
+
+    ch_versions = ch_versions.mix(TRGT_GENOTYPE.out.versions)
+    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
+    ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)
+    ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions)
+    ch_versions = ch_versions.mix(TRGT_PLOT.out.versions)
+
+    emit:
+    versions       = ch_versions
 }
diff --git a/subworkflows/local/utils_nfcore_pacvar_pipeline/main.nf b/subworkflows/local/utils_nfcore_pacvar_pipeline/main.nf
@@ -35,7 +35,6 @@ workflow PIPELINE_INITIALISATION {
 
 
     main:
-
     ch_versions = Channel.empty()
 
     //
Original file line number	Diff line number	Diff line change
Expand Up		@@ -35,7 +35,6 @@ workflow PIPELINE_INITIALISATION {


		main:

		ch_versions = Channel.empty()

		//
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