correct typos in nf_modules scripts

src/nf_modules/hisat2/mapping_paired.config

@@ -29,7 +29,7 @@ profiles {
         memory = "20GB"
         cpus = 32
         time = "12h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C"
         penv = "openmp32"
       }
     }

src/nf_modules/hisat2/mapping_paired.nf

 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 params.index = "$baseDir/data/index/*.index.*"
+params.output = "results/"
 
 log.info "fastq files : ${params.fastq}"
 log.info "index files : ${params.index}"
@@ -15,15 +16,15 @@ Channel
 
 process mapping_fastq {
   tag "$pair_id"
-  publishDir "results/mapping/", mode: 'copy'
+  publishDir "${params.output}", mode: 'copy'
 
   input:
-  set pair_id, file(reads) from fastq_files
+  set pair_id, file(fastq_filtred) from fastq_files
   file index from index_files.collect()
 
   output:
   file "*" into counts_files
-  set pair_id, "*.bam" into bam_files
+  set pair_id, "*.{bam, bai}" into bam_files
   file "*_report.txt" into mapping_report
 
   script:
@@ -34,15 +35,24 @@ process mapping_fastq {
     }
   }
 """
-hisat2 -p ${task.cpus} \
-  -x ${index_id} \
-  -1 ${reads[0]} \
-  -2 ${reads[1]} 2> \
-${pair_id}_hisat2_report.txt | \
-samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_hisat2_report.txt; then
+hisat2 -x ${index_id} \
+       -p ${task.cpus} \
+       -1 ${fastq_filtred[0]} \
+       -2 ${fastq_filtred[1]} \
+       --un-conc-gz ${pair_id}_notaligned_R%.fastq.gz \
+       --rna-strandness 'FR' \
+       --dta \
+       --no-softclip\
+       --trim3 1\
+       --trim5 1\
+       2> ${pair_id}_report.txt \
+| samtools view -bS -F 4 - \
+| samtools sort -@ ${task.cpus} -o ${pair_id}.bam \
+&& samtools index ${pair_id}.bam
+
+if grep -q "ERR" ${pair_id}.txt; then
   exit 1
 fi
+
 """
 }

src/nf_modules/kallisto/indexing.config

@@ -3,7 +3,7 @@ profiles {
     docker.temp = "auto"
     docker.enabled = true
     process {
-      withName index_fasta {
+      withName: index_fasta {
         container = "lbmc/kallisto:0.44.0"
         cpus = 4
       }

src/nf_modules/kallisto/indexing.nf

@@ -9,7 +9,7 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
+  publishDir "results/index/", mode: 'copy'
 
   input:
     file fasta from fasta_file

src/nf_modules/kallisto/mapping_paired.nf

 params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
 params.index = "$baseDir/data/index/*.index.*"
+params.output = "results/mapping/quantification/"
 
 log.info "fastq files : ${params.fastq}"
 log.info "index files : ${params.index}"
+log.info "output folder : ${params.output}"
 
 Channel
   .fromFilePairs( params.fastq )
@@ -15,7 +17,7 @@ Channel
 
 process mapping_fastq {
   tag "$reads"
-  publishDir "results/mapping/quantification/", mode: 'copy'
+  publishDir "${params.output}", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files