Commit a742b243 authored by Celine Noirot's avatar Celine Noirot

add quantification on prodigal and fraggenescan

parent 9b48fbbd
......@@ -549,8 +549,8 @@ process fraggenescan {
set replicateId, file(assembly_fna) from prokka_renamed2_fna_ch
output:
set replicateId, file("Sample_${replicateId}.gff") into fraggenescan_gff_ch
set replicateId, file("Sample_${replicateId}.log") into fraggenescan_count_ch
set file("Sample_${replicateId}.gff") into fraggenescan_gff_ch
set file("Sample_${replicateId}.log") into fraggenescan_count_ch
script:
"""
run_FragGeneScan.pl -genome=${assembly_fna} -out=Sample_${replicateId} -complete=1 -train=complete -thread=${task.cpus}
......@@ -574,8 +574,8 @@ process prodigal {
set replicateId, file(assembly_fna) from prokka_renamed3_fna_ch
output:
set replicateId, file("Sample_${replicateId}.gff") into prodigal_gff_ch
set replicateId, file("Sample_${replicateId}.log") into prodigal_count_ch
set file("Sample_${replicateId}.gff") into prodigal_gff_ch
set file("Sample_${replicateId}.log") into prodigal_count_ch
script:
"""
......@@ -658,8 +658,8 @@ prokka_reads_ch = prokka_renamed_gff_ch.join(prokka_renamed_fna_ch, remainder: t
set replicateId, file(gff_prokka), file(fna_prokka), file(filter_reads_R1), file(filter_reads_R2) from prokka_reads_ch
output:
file("${replicateId}.sort.bam") into reads_aligned_contigs_ch
file("${replicateId}.sort.bam.bai") into reads_aligned_contigs_index_ch
set replicateId,file("${replicateId}.sort.bam"),file("${replicateId}.sort.bam.bai") into reads_aligned_contigs_ch,reads_aligned_contigs2_ch
file("${replicateId}.featureCounts.tsv") into counts_ch
file("${replicateId}.featureCounts.tsv.summary") into featureCounts_out_ch
file("${replicateId}.featureCounts.stdout") into featureCounts_error_ch
......@@ -673,6 +673,39 @@ prokka_reads_ch = prokka_renamed_gff_ch.join(prokka_renamed_fna_ch, remainder: t
"""
}
process quantification_prodigal {
tag "${replicateId}"
publishDir "${params.outdir}/07_Quantification/prodigal", mode: 'copy'
input:
set replicateId, file(aln), file(aln_idx) from reads_aligned_contigs_ch
file(gff) from prodigal_gff_ch
output:
set replicateId, file("${replicateId}.prod.featureCounts.tsv"),file("${replicateId}.prod.featureCounts.tsv.summary"),file("${replicateId}.prod.featureCounts.stdout") into quantif_prod_ch
script:
"""
featureCounts -T ${task.cpus} -p -O -t CDS -g ID -a ${gff} -o ${replicateId}.prod.featureCounts.tsv ${aln} &> ${replicateId}.prod.featureCounts.stdout
"""
}
process quantification_fgs {
tag "${replicateId}"
publishDir "${params.outdir}/07_Quantification/fraggenescan", mode: 'copy'
input:
set replicateId, file(aln), file(aln_idx) from reads_aligned_contigs2_ch
file(gff) from fraggenescan_gff_ch
output:
set replicateId, file("${replicateId}.fgs.featureCounts.tsv"),file("${replicateId}.fgs.featureCounts.tsv.summary"),file("${replicateId}.fgs.featureCounts.stdout") into quantif_fgs_ch
script:
"""
featureCounts -T ${task.cpus} -p -O -t CDS -g ID -a ${gff} -o ${replicateId}.fgs.featureCounts.tsv ${aln} &> ${replicateId}.fgs.featureCounts.stdout
"""
}
// Create table with sum of reads for each global cluster of genes in each sample.
process quantification_table {
publishDir "${params.outdir}/07_Quantification", mode: 'copy'
......@@ -786,3 +819,4 @@ process diamond_parser {
aln2taxaffi.py -a ${prot_accession2taxid} --taxonomy ${taxonomy} -o ${replicateId} ${diamond_file} ${desman_len}
"""
}
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