[MODIF] fix input extension errors

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+* Fix recurrent bug in input file extension (#86)
 * Fix bug in `--bin_size` parameter (#85)
 * `min_mapq` is ignored if `--keep_multi` is used
 

main.nf

@@ -157,26 +157,36 @@ if (params.input_paths){
       .from( params.input_paths )
       .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
       .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
- }else{
 
+}else{
    raw_reads = Channel.create()
    raw_reads_2 = Channel.create()
 
-   Channel
-      .fromFilePairs( params.input )
-      .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
+   if ( params.split_fastq ){
+      Channel
+         .fromFilePairs( params.input, flat:true )
+         .splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
+         .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1]), tuple(a[0] + "_R2", a[2])] }
+   }else{
+      Channel
+         .fromFilePairs( params.input )
+	 .separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1][0]), tuple(a[0] + "_R2", a[1][1])] }
+   }
 }
 
-// SPlit fastq files
-// https://www.nextflow.io/docs/latest/operator.html#splitfastq
-
-if ( params.split_fastq ){
-   raw_reads_full = raw_reads.concat( raw_reads_2 )
-   raw_reads = raw_reads_full.splitFastq( by: params.fastq_chunks_size, file: true)
- }else{
-   raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag: "data")
+// Update sample name if splitFastq is used
+def updateSampleName(x) {
+   if ((matcher = x[1] =~ /\s*(\.[\d]+).fastq.gz/)) {
+        res = matcher[0][1]
+   }
+   return [x[0] + res, x[1]]
 }
 
+if (params.split_fastq ){
+  raw_reads = raw_reads.concat( raw_reads_2 ).map{it -> updateSampleName(it)}.dump(tag:'input')
+}else{
+  raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag:'input')
+}
 
 /*
  * Other input channels
@@ -230,7 +240,7 @@ else if ( params.fasta && params.restriction_site ){
            .ifEmpty { exit 1, "Restriction fragments: Fasta file not found: ${params.fasta}" }
            .set { fasta_for_resfrag }
 }
-else {
+else if (! params.dnase) {
     exit 1, "No restriction fragments file specified!"
 }
 
@@ -255,17 +265,17 @@ if (params.restriction_site){
    summary['Digestion']        = params.digestion
    summary['Restriction Motif']= params.restriction_site
    summary['Ligation Motif']   = params.ligation_site
-   summary['Min Fragment Size']= ("$params.min_restriction_fragment_size".isInteger() ? params.min_restriction_fragment_size : 'None')
-   summary['Max Fragment Size']= ("$params.max_restriction_fragment_size".isInteger() ? params.max_restriction_fragment_size : 'None')
-   summary['Min Insert Size']  = ("$params.min_insert_size".isInteger() ? params.min_insert_size : 'None')
-   summary['Max Insert Size']  = ("$params.max_insert_size".isInteger() ? params.max_insert_size : 'None')
+   summary['Min Fragment Size']= params.min_restriction_fragment_size
+   summary['Max Fragment Size']= params.max_restriction_fragment_size
+   summary['Min Insert Size']  = params.min_insert_size
+   summary['Max Insert Size']  = params.max_insert_size
 }else{
    summary['DNase Mode']    = params.dnase
-   summary['Min CIS dist']  = ("$params.min_cis_dist".isInteger() ? params.min_cis_dist : 'None')
+   summary['Min CIS dist']  = params.min_cis_dist
 }
 summary['Min MAPQ']         = params.min_mapq
-summary['Keep Duplicates']  = params.keep_dups
-summary['Keep Multihits']   = params.keep_multi
+summary['Keep Duplicates']  = params.keep_dups ? 'Yes' : 'No'
+summary['Keep Multihits']   = params.keep_multi ? 'Yes' : 'No'
 summary['Maps resolution']  = params.bin_size
 summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
 if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
@@ -435,7 +445,7 @@ if(!params.restriction_fragments && params.fasta && !params.dnase){
 */
 
 process bowtie2_end_to_end {
-   tag "$prefix"
+   tag "$sample"
    label 'process_medium'
    publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
    	      saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
@@ -445,13 +455,12 @@ process bowtie2_end_to_end {
    file index from bwt2_index_end2end.collect()
 
    output:
-   set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end
-   set val(prefix), file("${prefix}.bam") into end_to_end_bam
+   set val(sample), file("${prefix}_unmap.fastq") into unmapped_end_to_end
+   set val(sample), file("${prefix}.bam") into end_to_end_bam
 
    script:
    prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
    def bwt2_opts = params.bwt2_opts_end2end
-
    if (!params.dnase){
    """
    bowtie2 --rg-id BMG --rg SM:${prefix} \\
@@ -474,7 +483,7 @@ process bowtie2_end_to_end {
 }
 
 process trim_reads {
-   tag "$prefix"
+   tag "$sample"
    label 'process_low'
    publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
    	      saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
@@ -483,12 +492,13 @@ process trim_reads {
    !params.dnase
 
    input:
-   set val(prefix), file(reads) from unmapped_end_to_end
+   set val(sample), file(reads) from unmapped_end_to_end
 
    output:
-   set val(prefix), file("${prefix}_trimmed.fastq") into trimmed_reads
+   set val(sample), file("${prefix}_trimmed.fastq") into trimmed_reads
 
    script:
+   prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
    """
    cutsite_trimming --fastq $reads \\
                     --cutsite  ${params.ligation_site} \\
@@ -497,7 +507,7 @@ process trim_reads {
 }
 
 process bowtie2_on_trimmed_reads {
-   tag "$prefix"
+   tag "$sample"
    label 'process_medium'
    publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
    	      saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
@@ -506,11 +516,11 @@ process bowtie2_on_trimmed_reads {
    !params.dnase
 
    input:
-   set val(prefix), file(reads) from trimmed_reads
+   set val(sample), file(reads) from trimmed_reads
    file index from bwt2_index_trim.collect()
 
    output:
-   set val(prefix), file("${prefix}_trimmed.bam") into trimmed_bam
+   set val(sample), file("${prefix}_trimmed.bam") into trimmed_bam
 
    script:
    prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
@@ -524,22 +534,24 @@ process bowtie2_on_trimmed_reads {
 }
 
 if (!params.dnase){
-   process merge_mapping_steps{
-      tag "$sample = $bam1 + $bam2"
+   process bowtie2_merge_mapping_steps{
+      tag "$prefix = $bam1 + $bam2"
       label 'process_medium'
       publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
    	      saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
 
       input:
-      set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam )
+      set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam ).dump(tag:'merge')
 
       output:
       set val(sample), file("${prefix}_bwt2merged.bam") into bwt2_merged_bam
       set val(oname), file("${prefix}.mapstat") into all_mapstat
 
       script:
-      sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
-      tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
+      //sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
+      sample = prefix.toString() - ~/(_R1|_R2)/
+      //tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
+      tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
       oname = prefix.toString() - ~/(\.[0-9]+)$/
       """
       samtools merge -@ ${task.cpus} \\
@@ -566,46 +578,48 @@ if (!params.dnase){
    }
 }else{
    process dnase_mapping_stats{
-      tag "$sample = $bam1"
+      tag "$sample = $bam"
       label 'process_medium'
       publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
    	      saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
 
       input:
-      set val(prefix), file(bam1) from end_to_end_bam
+      set val(prefix), file(bam) from end_to_end_bam
 
       output:
-      set val(sample), file(bam1) into bwt2_merged_bam
+      set val(sample), file(bam) into bwt2_merged_bam
       set val(oname), file("${prefix}.mapstat") into all_mapstat
 
       script:
-      sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
-      tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
+      //sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
+      sample = prefix.toString() - ~/(_R1|_R2)/
+      //tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
+      tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
       oname = prefix.toString() - ~/(\.[0-9]+)$/
       """
       echo "## ${prefix}" > ${prefix}.mapstat
       echo -n "total_${tag}\t" >> ${prefix}.mapstat
-      samtools view -c ${bam1} >> ${prefix}.mapstat
+      samtools view -c ${bam} >> ${prefix}.mapstat
       echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
-      samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+      samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
       echo -n "global_${tag}\t" >> ${prefix}.mapstat
-      samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+      samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
       echo -n "local_${tag}\t0"  >> ${prefix}.mapstat
       """
    }
 }
 
-process combine_mapped_files{
+process combine_mates{
    tag "$sample = $r1_prefix + $r2_prefix"
    label 'process_low'
    publishDir "${params.outdir}/mapping", mode: params.publish_dir_mode,
    	      saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
 
    input:
-   set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'bams')
+   set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'mates')
 
    output:
-   set val(sample), file("${sample}_bwt2pairs.bam") into paired_bam
+   set val(oname), file("${sample}_bwt2pairs.bam") into paired_bam
    set val(oname), file("*.pairstat") into all_pairstat
 
    script:
@@ -629,7 +643,7 @@ process combine_mapped_files{
 
 /*
  * STEP2 - DETECT VALID PAIRS
-*/
+ */
 
 if (!params.dnase){
    process get_valid_interaction{
@@ -711,7 +725,7 @@ process remove_duplicates {
    	      saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$sample/$filename" : "$filename"}
 
    input:
-   set val(sample), file(vpairs) from valid_pairs.groupTuple()
+   set val(sample), file(vpairs) from valid_pairs.groupTuple().dump(tag:'final')
 
    output:
    set val(sample), file("*.allValidPairs") into all_valid_pairs