Fixing shortreads id getter

fmalmeida · Aug 18, 2020 · f7feef3 · f7feef3
1 parent 3f3649e
commit f7feef3
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Showing 3 changed files with 40 additions and 34 deletions.
diff --git a/main.nf b/main.nf
@@ -321,32 +321,32 @@ workflow pacbio_bas_nf {
     nanopack(pacbio_bam2fastq.out[0].flatten(), threads)
 }
 
-workflow paired_shortreads_nf {
+workflow shortreads_nf {
   take:
-    reads
+    preads
+    sreads
     threads
   main:
-    fastqc(reads, threads)
-    trimgalore(reads, threads)
-    if (params.lighter_execute && params.flash_execute) {
-      lighter(trimgalore.out[0], threads)
-      flash(lighter.out[0], threads)
-    } else if (params.lighter_execute && !params.flash_execute) {
-      lighter(trimgalore.out[0], threads)
-    } else if (!params.lighter_execute && params.flash_execute) {
-      flash(trimgalore.out[0], threads)
+    fastqc(preads, sreads, threads)
+    trimgalore(preads, sreads, threads)
+
+    // Paired
+    if (params.shortreads_type == 'paired') {
+      if (params.lighter_execute && params.flash_execute) {
+        lighter(trimgalore.out[0], threads)
+        flash(lighter.out[0], threads)
+      } else if (params.lighter_execute && !params.flash_execute) {
+        lighter(trimgalore.out[0], threads)
+      } else if (!params.lighter_execute && params.flash_execute) {
+        flash(trimgalore.out[0], threads)
+      }
     }
-}
 
-workflow single_shortreads_nf {
-  take:
-    reads
-    threads
-  main:
-    fastqc(reads, threads)
-    trimgalore(reads, threads)
-    if (params.lighter_execute) {
-      lighter(trimgalore.out[1].flatten(), threads)
+    // Single
+    if (params.shortreads_type == 'paired') {
+      if (params.lighter_execute) {
+        lighter(trimgalore.out[1].flatten(), threads)
+      }
     }
 }
 
@@ -387,14 +387,15 @@ workflow {
    * User has short paired end reads
    */
   if (params.shortreads && params.shortreads_type == 'paired') {
-    paired_shortreads_nf(Channel.fromFilePairs(params.shortreads, flat: true, size: 2), params.threads)
+    shortreads_nf(Channel.fromFilePairs(params.shortreads, flat: true, size: 2),
+                  Channel.value(''), params.threads)
   }
 
   /*
    * User has short single end reads
    */
   if (params.shortreads && params.shortreads_type == 'single') {
-    single_shortreads_nf(Channel.fromPath(params.shortreads), params.threads)
+    shortreads_nf(Channel.value(['', '', '']), Channel.fromPath(params.shortreads), params.threads)
   }
 }
 

diff --git a/modules/fastqc.nf b/modules/fastqc.nf
@@ -4,19 +4,23 @@ process fastqc {
   tag "Evaluating short reads with FastQC"
 
     input:
-      file reads
+      tuple val(id), file(read1), file(read2)
+      file(sreads)
       val threads
+
     output:
       file "fastqc_${id}/*_fastqc.{zip,html}"
+
     script:
+
       if (params.shortreads_type == 'paired') {
-        id = (reads[1].getBaseName() - "_1")
-        param = "-q ${reads[1]} ${reads[2]}"
+        param = "-q ${read1} ${read2}"
       }
       else if (params.shortreads_type == 'single') {
-        param = "-q ${reads}"
-        id = reads.getBaseName()
+        param = "-q ${sreads}"
+        id = sreads.getBaseName()
       }
+
     """
     mkdir fastqc_${id} ;
     fastqc -t $threads -o fastqc_${id} $param

diff --git a/modules/trimgalore.nf b/modules/trimgalore.nf
@@ -8,11 +8,13 @@ process trimgalore {
             else null
         }
     container 'fmalmeida/ngs-preprocess'
-    tag "Executing TrimGalore with paired end reads."
+    tag "Executing TrimGalore"
 
     input:
-      file reads
-      file threads
+      tuple val(id), file(read1), file(read2)
+      file(sreads)
+      val threads
+
     output:
       tuple val('trimgalore'), file("${id}_1.fq.gz"), file("${id}_2.fq.gz") optional true
       file "*.fq.gz" optional true
@@ -27,12 +29,11 @@ process trimgalore {
       tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
 
       if (params.shortreads_type == 'paired') {
-        id = (reads[1].getBaseName() - "_1")
-        param = "--paired $c_r1 $c_r2 $tpc_r1 $tpc_r2 ${reads[1]} ${reads[2]}"
+        param = "--paired $c_r1 $c_r2 $tpc_r1 $tpc_r2 ${read1} ${read2}"
         rename = "mv *_val_1.fq.gz ${id}_1.fq.gz ; mv *_val_2.fq.gz ${id}_2.fq.gz"
       }
       else if (params.shortreads_type == 'single') {
-        param = "$c_r1 $tpc_r1 ${reads}"
+        param = "$c_r1 $tpc_r1 ${sreads}"
         id = reads.getBaseName()
         rename = ''
       }