diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index b5d075de66d926e2c5cd79ee8992bd1f79c45959..a50a75ee42199285c5f4ed4eb80831fe8e547224 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -1,10 +1,15 @@
version = "1.11"
container_url = "lbmc/samtools:${version}"
+params.index_fasta = ""
+params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(fasta)
@@ -13,16 +18,20 @@ process index_fasta {
script:
"""
-samtools faidx ${fasta}
+samtools faidx ${params.index_fasta} ${fasta}
"""
}
-filter_bam_quality_threshold = 30
-
+params.filter_bam_quality_threshold = 30
+params.filter_bam_quality = "-q ${filter_bam_quality_threshold}"
+params.filter_bam_quality_out = ""
process filter_bam_quality {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -31,16 +40,20 @@ process filter_bam_quality {
tuple val(file_id), path("*_filtered.bam"), emit: bam
script:
"""
-samtools view -@ ${task.cpus} -hb ${bam} -q ${filter_bam_quality_threshold} > \
+samtools view -@ ${task.cpus} -hb ${bam} ${params.filter_bam_quality} > \
${bam.simpleName}_filtered.bam
"""
}
-
+params.filter_bam = ""
+params.filter_bam_out = ""
process filter_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -50,11 +63,13 @@ process filter_bam {
tuple val(file_id), path("*_filtered.bam"), emit: bam
script:
"""
-samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > \
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} ${params.filter_bam} > \
${bam.simpleName}_filtered.bam
"""
}
+params.filter_bam_mapped = "-F 4"
+params.filter_bam_mapped_out = ""
process filter_bam_mapped {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -67,15 +82,20 @@ process filter_bam_mapped {
tuple val(file_id), path("*_mapped.bam"), emit: bam
script:
"""
-samtools view -@ ${task.cpus} -F 4 -hb ${bam} > \
+samtools view -@ ${task.cpus} ${params.filter_bam_mapped} -hb ${bam} > \
${bam.simpleName}_mapped.bam
"""
}
+params.filter_bam_unmapped = "-f 4"
+params.filter_bam_unmapped_out = ""
process filter_bam_unmapped {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -84,11 +104,12 @@ process filter_bam_unmapped {
tuple val(file_id), path("*_unmapped.bam"), emit: bam
script:
"""
-samtools view -@ ${task.cpus} -f 4 -hb ${bam} > ${bam.simpleName}_unmapped.bam
+samtools view -@ ${task.cpus} ${params.filter_bam_unmapped} -hb ${bam} > ${bam.simpleName}_unmapped.bam
"""
}
-
+params.index_bam = ""
+params.index_bam_out = ""
process index_bam {
container = "${container_url}"
label "big_mem_mono_cpus"
@@ -103,14 +124,19 @@ process index_bam {
script:
"""
-samtools index ${bam}
+samtools index ${params.index_bam} ${bam}
"""
}
+params.sort_bam = ""
+params.sort_bam_out = ""
process sort_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -120,15 +146,19 @@ process sort_bam {
script:
"""
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.simpleName}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} ${params.sort_bam} -O BAM -o ${bam.simpleName}_sorted.bam ${bam}
"""
}
-
+params.split_bam = ""
+params.split_bam_out = ""
process split_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -138,19 +168,22 @@ process split_bam {
tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
script:
"""
-samtools view --@ ${Math.round(task.cpus/2)} \
+samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -F 0x10 ${bam} > ${bam.simpleName}_forward.bam &
-samtools view --@ ${Math.round(task.cpus/2)} \
+samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -f 0x10 ${bam} > ${bam.simpleName}_reverse.bam
"""
}
-
+params.merge_bam = ""
+params.merge_bam_out = ""
process merge_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
- cpus = 2
+ if (params.mapping_fastq_out != "") {
+ publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(first_file_id), path(first_bam)
@@ -160,16 +193,20 @@ process merge_bam {
tuple val(file_id), path("*.bam*"), emit: bam
script:
"""
-samtools merge ${first_bam} ${second_bam} \
+samtools merge -@ ${task.cpus} ${params.merge_bam} ${first_bam} ${second_bam} \
${first_bam.simpleName}_${second_file.simpleName}.bam
"""
}
+params.merge_multi_bam = ""
+params.merge_multi_bam_out = ""
process merge_multi_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
- cpus = 2
+ if (params.mapping_fastq_out != "") {
+ publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bams)
@@ -179,16 +216,21 @@ process merge_multi_bam {
script:
"""
samtools merge -@ ${task.cpus} \
+ ${params.merge_multi_bam} \
${bams[0].simpleName}_merged.bam \
${bams}
"""
}
+params.stats_bam = ""
+params.stats_bam_out = ""
process stats_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
- cpus = 2
+ if (params.mapping_fastq_out != "") {
+ publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -197,12 +239,17 @@ process stats_bam {
tuple val(file_id), path("*.tsv"), emit: tsv
script:
"""
-samtools flagstat -@ ${task.cpus} -O tsv ${bam} > ${bam.simpleName}_stats.tsv
+samtools flagstat -@ ${task.cpus} ${params.stats_bam} -O tsv ${bam} > ${bam.simpleName}_stats.tsv
"""
}
+params.flagstat_2_multiqc = ""
+params.flagstat_2_multiqc_out = ""
process flagstat_2_multiqc {
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(tsv)
@@ -214,8 +261,13 @@ mv ${tsv} ${tsv.simpleName}.flagstat.txt
"""
}
+params.idxstat_2_multiqc = ""
+params.idxstat_2_multiqc_out = ""
process idxstat_2_multiqc {
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(tsv)
diff --git a/src/nf_modules/sratoolkit/main.nf b/src/nf_modules/sratoolkit/main.nf
index 3396d6e3e749eca10e6d69b3aa72e47ef81217f1..158d4058764560e9771133952db53b70391182c9 100644
--- a/src/nf_modules/sratoolkit/main.nf
+++ b/src/nf_modules/sratoolkit/main.nf
@@ -1,10 +1,15 @@
version = "2.8.2"
container_url = "lbmc/sratoolkit:${version}"
+params.fastq_dump = ""
+params.fastq_dump_out = ""
process fastq_dump {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$sra"
+ if (params.fastq_dump_out != "") {
+ publishDir "results/${params.fastq_dump_out}", mode: 'copy'
+ }
input:
val sra
@@ -14,7 +19,7 @@ process fastq_dump {
script:
"""
-fastq-dump --split-files --gzip ${sra}
+fastq-dump ${params.fastq_dump} --split-files --gzip ${sra}
if [ -f ${sra}_1.fastq ]
then
mv ${sra}_1.fastq ${sra}_R1.fastq
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 1e9debe3206e2bf3e83b645b0b060105fce63038..bba183435efcbb1036a399aa171af76fa834624a 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -2,10 +2,14 @@ version = "407"
container_url = "lbmc/ucsc:${version}"
params.bedgraph_to_bigwig = ""
+params.bedgraph_to_bigwig_out = ""
process bedgraph_to_bigwig {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
+ if (params.bedgraph_to_bigwig_out != "") {
+ publishDir "results/${params.bedgraph_to_bigwig_out}", mode: 'copy'
+ }
input:
tuple val(file_id) path(bg)
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
index 48200cc0487938db3c8295e12c5077d8e721b39d..94279df885615b280b90fab8926453b4fd470021 100644
--- a/src/nf_modules/urqt/main.nf
+++ b/src/nf_modules/urqt/main.nf
@@ -3,74 +3,37 @@ container_url = "lbmc/urqt:${version}"
trim_quality = "20"
+params.trimming = "--t 20"
process trimming {
container = "${container_url}"
label "big_mem_multi_cpus"
- tag "${reads}"
+ tag "${file_id}"
input:
- tuple val(pair_id), path(reads)
-
- output:
- tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq
- path "*_report.txt", emit: report
-
- script:
-if (reads instanceof List)
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
- --in ${reads[0]} --inpair ${reads[1]} \
- --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
- > ${pair_id}_trimming_report.txt
-"""
-else
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
- --in ${reads} \
- --out ${file_id}_trim.fastq.gz \
- > ${file_id}_trimming_report.txt
-"""
-}
-
-process trimming_pairedend {
- container = "${container_url}"
- label "big_mem_multi_cpus"
- tag "${reads}"
-
- input:
- tuple val(pair_id), path(reads)
+ tuple val(file_id), path(reads)
output:
tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
+ }
+ if (reads.size() == 2)
+"""
+UrQt ${params.trimming} --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
- --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+ --out ${file_prefix}_trim_R1.fastq.gz --outpair ${file_prefix}_trim_R2.fastq.gz \
> ${pair_id}_trimming_report.txt
"""
-}
-
-process trimming_singleend {
- container = "${container_url}"
- label "big_mem_multi_cpus"
- tag "$file_id"
-
- input:
- tuple val(file_id), path(reads)
-
- output:
- tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
- path "*_report.txt", emit: report
-
- script:
+ else if (reads.size() == 1)
"""
-UrQt --t 20 --m ${task.cpus} --gz \
- --in ${reads} \
- --out ${file_id}_trim.fastq.gz \
- > ${file_id}_trimming_report.txt
+UrQt ${params.trimming} --m ${task.cpus} --gz \
+ --in ${reads[0]} \
+ --out ${file_prefix}_trim.fastq.gz \
+ > ${file_prefix}_trimming_report.txt
"""
-}
-
+}
\ No newline at end of file