Remove antibody variable reference in DESeq2 module

Author: drpatelh

conf/modules.config

@@ -690,6 +690,7 @@ if (!params.skip_consensus_peaks) {
                     '--count_col 7',
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim()
+                ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
                     path: { [
                         "${params.outdir}/${params.aligner}/mergedLibrary/macs2",

modules/local/deseq2_qc.nf

@@ -27,8 +27,7 @@ process DESEQ2_QC {
     script:
     def args      = task.ext.args ?: ''
     def peak_type = params.narrow_peak ? 'narrowPeak' : 'broadPeak'
-    def antibody  = meta.antibody
-    def prefix    = "${antibody}.consensus_peaks"
+    def prefix    = task.ext.prefix ?: "${meta.id}"
     """
     deseq2_qc.r \\
         --count_file $counts \\
@@ -38,11 +37,11 @@ process DESEQ2_QC {
         $args
 
     sed 's/deseq2_pca/deseq2_pca_${task.index}/g' <$deseq2_pca_header >tmp.txt
-    sed -i -e 's/DESeq2 /${antibody} DESeq2 /g' tmp.txt
+    sed -i -e 's/DESeq2 /${meta.id} DESeq2 /g' tmp.txt
     cat tmp.txt ${prefix}.pca.vals.txt > ${prefix}.pca.vals_mqc.tsv
 
     sed 's/deseq2_clustering/deseq2_clustering_${task.index}/g' <$deseq2_clustering_header >tmp.txt
-    sed -i -e 's/DESeq2 /${antibody} DESeq2 /g' tmp.txt
+    sed -i -e 's/DESeq2 /${meta.id} DESeq2 /g' tmp.txt
     cat tmp.txt ${prefix}.sample.dists.txt > ${prefix}.sample.dists_mqc.tsv
 
     cat <<-END_VERSIONS > versions.yml