Output versions.yml file where topic channels not implemented yet

Author: JoseEspinosa

main.nf

@@ -66,6 +66,7 @@ workflow NFCORE_CHIPSEQ {
         params.chromap_index,
         params.star_index,
     )
+    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
 
     //
     // WORKFLOW: Run nf-core/chipseq workflow
@@ -89,7 +90,6 @@ workflow NFCORE_CHIPSEQ {
 
     emit:
     multiqc_report = CHIPSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
-    versions       = ch_versions                // channel: [version1, version2, ...]
 }
 
 /*

subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf

@@ -26,6 +26,8 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
 
     main:
 
+    ch_versions = channel.empty()
+
     //
     // Call peaks with MACS3
     //
@@ -79,6 +81,7 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
         ch_peak_count_header_multiqc,
         ch_frip_score_multiqc
     )
+    ch_versions = ch_versions.mix(MULTIQC_CUSTOM_PEAKS.out.versions.first())
 
     ch_homer_annotatepeaks          = channel.empty()
     ch_plot_macs3_qc_txt            = channel.empty()
@@ -96,6 +99,7 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
             ch_gtf
         )
         ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt
+        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first())
 
         if (!skip_peak_qc) {
             //
@@ -142,4 +146,6 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
     plot_homer_annotatepeaks_txt = ch_plot_homer_annotatepeaks_txt  // channel: [ txt ]
     plot_homer_annotatepeaks_pdf = ch_plot_homer_annotatepeaks_pdf  // channel: [ pdf ]
     plot_homer_annotatepeaks_tsv = ch_plot_homer_annotatepeaks_tsv  // channel: [ tsv ]
+
+    versions                     = ch_versions                      // channel: [ versions.yml ]
 }

subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2/main.nf

@@ -23,6 +23,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
 
     main:
 
+    ch_versions = channel.empty()
 
     // Create channels: [ meta , [ peaks ] ]
     // Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
@@ -67,13 +68,15 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
             ch_fasta,
             ch_gtf
         )
+        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions)
 
         //
         // MODULE: Add boolean fields to annotated consensus peaks to aid filtering
         //
         ANNOTATE_BOOLEAN_PEAKS (
             MACS3_CONSENSUS.out.boolean_txt.join(HOMER_ANNOTATEPEAKS.out.txt, by: [0]),
         )
+        ch_versions = ch_versions.mix(ANNOTATE_BOOLEAN_PEAKS.out.versions)
     }
 
     // Create channels: [ meta, [ ip_bams ], saf ]
@@ -86,7 +89,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
         }
         .join(ch_bams)
         .map {
-            antibody, meta, saf, bams, meta_single_end ->
+            _antibody, meta, saf, bams, meta_single_end ->
                 [ meta + meta_single_end, bams.flatten().sort(), saf ]
         }
         .set { ch_bam_saf }
@@ -125,6 +128,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
         ch_deseq2_qc_dists_multiqc = DESEQ2_QC.out.dists_multiqc
         ch_deseq2_qc_log           = DESEQ2_QC.out.log
         ch_deseq2_qc_size_factors  = DESEQ2_QC.out.size_factors
+        ch_versions = ch_versions.mix(DESEQ2_QC.out.versions)
     }
 
     emit:
@@ -147,4 +151,6 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
     deseq2_qc_dists_multiqc = ch_deseq2_qc_dists_multiqc        // channel: [ txt ]
     deseq2_qc_log           = ch_deseq2_qc_log                  // channel: [ txt ]
     deseq2_qc_size_factors  = ch_deseq2_qc_size_factors         // channel: [ txt ]
+
+    versions                = ch_versions                       // channel: [ versions.yml ]
 }

subworkflows/local/prepare_genome/main.nf

@@ -40,6 +40,8 @@ workflow PREPARE_GENOME {
 
     main:
 
+    ch_versions = channel.empty()
+
     //
     // Uncompress genome fasta file if required
     //
@@ -100,6 +102,7 @@ workflow PREPARE_GENOME {
 
     if (make_bed) {
         ch_gene_bed = GTF2BED(ch_gtf).bed
+        ch_versions = ch_versions.mix(GTF2BED.out.versions)
     } else {
         if (gene_bed.endsWith('.gz')) {
             ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
@@ -204,4 +207,5 @@ workflow PREPARE_GENOME {
     bowtie2_index = ch_bowtie2_index          //    path: bowtie2/index/
     chromap_index = ch_chromap_index          //    path: genome.index
     star_index    = ch_star_index             //    path: star/index/
+    versions      = ch_versions       //    path: versions.yml
 }

workflows/chipseq.nf

@@ -462,6 +462,7 @@ workflow CHIPSEQ {
         params.skip_peak_annotation,
         params.skip_peak_qc
     )
+    ch_versions = ch_versions.mix(BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER.out.versions)
 
     //
     //  Consensus peaks analysis
@@ -501,6 +502,7 @@ workflow CHIPSEQ {
         ch_subreadfeaturecounts_multiqc  = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.featurecounts_summary
         ch_deseq2_pca_multiqc            = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_pca_multiqc
         ch_deseq2_clustering_multiqc     = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_dists_multiqc
+        ch_versions = ch_versions.mix(BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.versions)
     }
 
     //
@@ -516,11 +518,15 @@ workflow CHIPSEQ {
             ch_macs3_consensus_bed_lib.collect{it[1]}.ifEmpty([]),
             ch_macs3_consensus_txt_lib.collect{it[1]}.ifEmpty([])
         )
+        ch_versions = ch_versions.mix(IGV.out.versions)
     }
 
     //
     // Collate and save software versions
     //
+    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+    ch_versions = ch_versions.mix(BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER.out.versions)
+
     ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
         .mix(topic_versions_string)
         .collectFile(