Skip alignment in other processes

main.nf

@@ -811,27 +811,29 @@ if(params.aligner == 'hisat2' && !params.skip_alignment){
  samtools index ${hisat2_bam.baseName}.sorted.bam
  """
  }
+}
 
- process sort_by_name_BAM {
-  tag "${bam_featurecounts.baseName - '.sorted'}"
+process sort_by_name_BAM {
+ tag "${bam_featurecounts.baseName - '.sorted'}"
 
-  input:
-  file bam_featurecounts
+ when:
+ !params.skip_alignment
 
-  output:
-  file "${bam_featurecounts.baseName}ByName.bam" into bam_featurecounts_sorted, bam_count_exons
+ input:
+ file bam_featurecounts
 
- script:
- def avail_mem = task.memory ? "-m ${task.memory.toBytes() / (task.cpus + 2)}" : ''
- """
- samtools sort -n \\
- $bam_featurecounts \\
- -@ ${task.cpus} $avail_mem \\
- -o ${bam_featurecounts.baseName}ByName.bam
- """
- }
-}
+ output:
+ file "${bam_featurecounts.baseName}ByName.bam" into bam_featurecounts_sorted, bam_count_exons
 
+ script:
+ def avail_mem = task.memory ? "-m ${task.memory.toBytes() / (task.cpus + 2)}" : ''
+ """
+ samtools sort -n \\
+ $bam_featurecounts \\
+ -@ ${task.cpus} $avail_mem \\
+ -o ${bam_featurecounts.baseName}ByName.bam
+ """
+}
 
 /*
  * STEP 3Salmon.1 - quant transcripts with Salmon
@@ -911,7 +913,7 @@ if(params.run_salmon || params.run_txrevise ){
 /*
  * Leafcutter quantification preparation step
  */
-if(params.run_leafcutter){
+if(params.run_leafcutter && !params.skip_alignment){
  process leafcutter_bam_to_junc {
  tag "${leafcutter_bam.baseName}"
 
@@ -932,7 +934,7 @@ if(params.run_leafcutter){
 /*
  * Leafcutter quantification step
  */
-if(params.run_leafcutter){
+if(params.run_leafcutter && !params.skip_alignment){
  process leafcutter_cluster_junctions {
  tag "${junc_files.baseName}"
  publishDir "${params.outdir}/leafcutter", mode: 'copy'
@@ -957,7 +959,7 @@ if(params.run_leafcutter){
 /*
  * Quantify exon expression - featureCounts (exon level)
  */
-if (params.run_exon_quant){
+if (params.run_exon_quant && !params.skip_alignment){
  process count_exons {
  tag "${bam.simpleName}"
  publishDir "${params.outdir}/dexseq_exon_counts/quant_files", mode: 'copy'
@@ -985,7 +987,7 @@ if (params.run_exon_quant){
 /*
  * Merge exon counts files
  */
-if(params.run_exon_quant){
+if(params.run_exon_quant && !params.skip_alignment){
  process exon_count_merge {
  tag "merge exon ${input_files.size()} files"
  publishDir "${params.outdir}/dexseq_exon_counts", mode: 'copy'
@@ -1009,7 +1011,7 @@ if(params.run_exon_quant){
 /*
  * Run QTLtools MBV
  */
-if(params.run_mbv){
+if(params.run_mbv && !params.skip_alignment){
  process run_mbv {
  tag "${mbv_bam.simpleName}"
  publishDir "${params.outdir}/MBV", mode: 'copy'
@@ -1255,6 +1257,9 @@ process featureCounts {
  else if (filename.indexOf("_gene.featureCounts.txt") > 0) "gene_counts/$filename"
  else "$filename"
  }
+
+ when:
+ !params.skip_alignment
 
  input:
  file bam_featurecounts_sorted
@@ -1292,6 +1297,9 @@ process merge_featureCounts {
  tag "merge ${input_files.size()} files"
  publishDir "${params.outdir}/featureCounts", mode: 'copy'
 
+ when:
+ !params.skip_alignment
+
  input:
  file input_files from featureCounts_to_merge.toSortedList()
 
@@ -1315,7 +1323,7 @@ process sample_correlation {
  publishDir "${params.outdir}/sample_correlation", mode: 'copy'
 
  when:
- !params.skip_qc && !params.skip_edger
+ !params.skip_qc && !params.skip_edger && !params.skip_alignment
 
  input:
  file input_files from geneCounts.collect()