Add antibody directory to consensus peaks in IGV session

Author: drpatelh

modules/local/igv.nf

@@ -9,28 +9,31 @@ process IGV {
         'quay.io/biocontainers/python:3.8.3' }"
 
     input:
+    val aligner_dir
+    val peak_dir
     path fasta
-    path ("${bigwig_publish_dir}/*")
-    path ("${peak_publish_dir}/*")
-    path ("${consensus_publish_dir}/*")
-    val bigwig_publish_dir
-    val peak_publish_dir
-    val consensus_publish_dir
-
+    path ("${aligner_dir}/mergedLibrary/bigwig/*")
+    path ("${aligner_dir}/mergedLibrary/macs2/${peak_dir}/*")
+    path ("${aligner_dir}/mergedLibrary/macs2/${peak_dir}/consensus/*")
+    path ("mappings/*")
+    
     output:
     path "*files.txt"  , emit: txt
     path "*.xml"       , emit: xml
     path "versions.yml", emit: versions
 
     script: // scripts are bundled with the pipeline in nf-core/chipseq/bin/
+    def consensus_dir = "${aligner_dir}/mergedLibrary/macs2/${peak_dir}/consensus/*"
     """
     find * -type l -name "*.bigWig" -exec echo -e ""{}"\\t0,0,178" \\; > bigwig.igv.txt
     find * -type l -name "*Peak" -exec echo -e ""{}"\\t0,0,178" \\; > peaks.igv.txt
     # Avoid error when consensus not produced
-    find * -type l -name "*.bed" -exec echo -e ""{}"\\t0,0,178" \\; | { grep "^$consensus_publish_dir" || test \$? = 1; } > bed.igv.txt
+    find * -type l -name "*.bed" -exec echo -e ""{}"\\t0,0,178" \\; | { grep "^$consensus_dir" || test \$? = 1; } > consensus.igv.txt
+
+    cat mappings/* > replace_paths.txt
 
-    cat *.txt > igv_files.txt
-    igv_files_to_session.py igv_session.xml igv_files.txt ../../genome/${fasta.getName()} --path_prefix '../../'
+    cat *.igv.txt > igv_files_orig.txt
+    igv_files_to_session.py igv_session.xml igv_files_orig.txt replace_paths.txt ../../genome/${fasta.getName()} --path_prefix '../../'
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/macs2_consensus.nf

@@ -17,6 +17,7 @@ process MACS2_CONSENSUS {
     tuple val(meta), path("*.bed")          , emit: bed
     tuple val(meta), path("*.saf")          , emit: saf
     tuple val(meta), path("*.pdf")          , emit: pdf
+    tuple val(meta), path("*.antibody.txt") , emit: txt
     tuple val(meta), path("*.boolean.txt")  , emit: boolean_txt
     tuple val(meta), path("*.intersect.txt"), emit: intersect_txt
     path "versions.yml"                     , emit: versions
@@ -25,7 +26,6 @@ process MACS2_CONSENSUS {
     task.ext.when == null || task.ext.when
 
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
-
     def prefix       = task.ext.prefix    ?: "${meta.id}"
     def peak_type    = params.narrow_peak ? 'narrowPeak' : 'broadPeak'
     def mergecols    = params.narrow_peak ? (2..10).join(',') : (2..9).join(',')
@@ -49,6 +49,8 @@ process MACS2_CONSENSUS {
 
     plot_peak_intersect.r -i ${prefix}.boolean.intersect.txt -o ${prefix}.boolean.intersect.plot.pdf
 
+    echo "${prefix}.bed\t${meta.id}/${prefix}.bed" > ${prefix}.antibody.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')

workflows/chipseq.nf

@@ -543,6 +543,7 @@ workflow CHIPSEQ {
     //  Consensus peaks analysis
     //
     ch_macs2_consensus_bed_lib   = Channel.empty()
+    ch_macs2_consensus_txt_lib   = Channel.empty()
     ch_deseq2_pca_multiqc        = Channel.empty()
     ch_deseq2_clustering_multiqc = Channel.empty()
     if (!params.skip_consensus_peaks) {
@@ -579,6 +580,7 @@ workflow CHIPSEQ {
             ch_antibody_peaks
         )
         ch_macs2_consensus_bed_lib = MACS2_CONSENSUS.out.bed
+        ch_macs2_consensus_txt_lib = MACS2_CONSENSUS.out.txt
         ch_versions = ch_versions.mix(MACS2_CONSENSUS.out.versions)
 
         if (!params.skip_peak_annotation) {
@@ -653,26 +655,13 @@ workflow CHIPSEQ {
     //
     if (!params.skip_igv) {
         IGV (
+            params.aligner,
+            params.narrow_peak ? 'narrowPeak' : 'broadPeak',
             PREPARE_GENOME.out.fasta,
             UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([]),
             ch_macs2_peaks.collect{it[1]}.ifEmpty([]),
             ch_macs2_consensus_bed_lib.collect{it[1]}.ifEmpty([]),
-            { "${params.aligner}/mergedLibrary/bigwig" },
-            { 
-                [
-                    "${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak ? '/narrowPeak' : '/broadPeak'
-                ]
-                .join('') 
-            },
-            { 
-                [
-                    "${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak ? '/narrowPeak' : '/broadPeak',
-                    '/consensus'
-                ]
-                .join('') 
-            }
+            ch_macs2_consensus_txt_lib.collect{it[1]}.ifEmpty([])
         )
         ch_versions = ch_versions.mix(IGV.out.versions)
     }