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Merge branch 'dev' of https://github.com/number-25/rich_directRNA into dev
2 parents 40634d3 + b9cf698 commit fe29bd5

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Lines changed: 126 additions & 67 deletions

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‎.gitattributes‎

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*.nf.test linguist-language=nextflow
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated
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*.html linguist-generated=true

‎modules/local/sqanti/qc/main.nf‎

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process QC_SQANTI {
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process SQANTI_QC {
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tag "$meta.id"
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label 'process_high'
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'anaconesalab/sqanti3:5.3.6-conda-fix'"
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'anaconesalab/sqanti3:v5.5.1"
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input:
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tuple val(meta), path(reconstructed_transcriptome)
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path annotation_gtf
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tuple path(genome_fasta), path(genome_fasta_index)
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val program
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val reconstruction_program
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output:
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// Substantial outputs list
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path "refAnnotation_*.genePred", optional: yes
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path "*.params.txt"
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path "*_classification.txt"
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path "*_corrected.faa"
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path "*_corrected.fasta"
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path "*_corrected.genePred", optional: yes
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path "*.corrected.gtf"
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path "*.corrected.gtf.cds.gff"
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path "*.html", optional: yes
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path "*.pdf", optional: yes
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path "*.junctions.txt", optional: yes
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path "isoforms_classification.txt"
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path "isoforms_corrected.cds.gff3"
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path "isoforms_corrected.faa"
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path "isoforms_corrected.fasta"
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path "isoforms_corrected.genePred"
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tuple val(meta), path "isoforms_corrected.gtf", emit: sqanti_qc_isoforms_gtf
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path "isoforms_junctions.txt"
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path "isoforms.qc_params.txt"
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path "refAnnotation_isoforms.genePred"
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path "unknown_strand.gtf"
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path "GMST"
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path "RTS"
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path "versions.yml" , emit: versions
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//path "logs/final_report.log"
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//path "logs/gtf2fasta.log
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//path "logs/GTF_to_genePred.log"
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//path "logs/normalize_gtf.log"
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//path "logs/sqanti3_qc.log"
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//path "logs/TD2_LongOrfs.log"
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//path "logs/TD2_Predict.log"
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path "RTS/sj.rts.results.tsv" , optional: yes
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path "TD2/isoforms_corrected.fasta.TD2.bed" , optional: yes
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path "TD2/isoforms_corrected.fasta.TD2.cds" , optional: yes
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path "TD2/isoforms_corrected.fasta.TD2.gff2" , optional: yes
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path "TD2/longest_orfs.cds" , optional: yes
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path "TD2/longest_orfs.gff2" , optional: yes
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path "TD2/longest_orfs.pep" , optional: yes
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path "TD2/psauron_score.csv" , optional: yes
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def output_name = task.ext.out_name ?: "--output ${program}"
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def prefix = task.ext.prefix ?: "${meta.id}.${meta.replicate}_${program}_sqantiQC"
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def prefix = task.ext.prefix ?:
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"${meta.id}.${meta.replicate}_${reconstruction_ program}_sqantiQC"
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"""
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sqantiqc.py \\
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$reconstructed_transcriptome \\
@@ -55,25 +66,27 @@ process QC_SQANTI {
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def output_name = task.ext.out_name ?: "--output ${program}"
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def prefix = task.ext.prefix ?: "${meta.id}.${meta.replicate}_${program}_sqantiQC"
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"""
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mkdir GMST
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touch GMST/gms.log
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touch GMST/GMST_tmp
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touch GMST/GMST_tmp.faa
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touch GMST/GMST_tmp.fnn
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touch isoforms_classification.txt
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touch isoforms_corrected.cds.gff3
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touch isoforms_corrected.faa
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touch isoforms_corrected.fasta
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touch isoforms_corrected.genePred
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touch isoforms_corrected.gtf
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touch isoforms_junctions.txt
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touch isoforms.qc_params.txt
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touch refAnnotation_isoforms.genePred
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touch unknown_strand.gtf
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mkdir logs
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mkdir RTS
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touch RTS/sj.rts.results.tsv
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touch unknown_strand.gtf
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touch ${program}_SQANTI3_report.html
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touch ${program}_SQANTI3_report.pdf
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touch ${program}_junctions.txt
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touch ${program}_corrected.gtf.cds.gff
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touch ${program}_corrected.gtf
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touch ${program}_corrected.genePred
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touch ${program}_corrected.fasta
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touch ${program}_corrected.faa
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touch ${program}_classification.txt
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touch ${program}.params.txt
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touch refAnnotation_${program}.genePred
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mkdir TD2
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touch TD2/isoforms_corrected.fasta.TD2.bed
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touch TD2/isoforms_corrected.fasta.TD2.cds
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touch TD2/isoforms_corrected.fasta.TD2.gff2
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touch TD2/longest_orfs.cds
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touch TD2/longest_orfs.gff2
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touch TD2/longest_orfs.pep
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touch TD2/psauron_score.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":

‎sqanti3_trial_run/run_sqanti3_qc.sh‎

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This file was deleted.

‎subworkflows/local/sqanti/main.nf‎

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//****************************************************************************
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//* SUBWORKFLOW: SQANTI - ALL
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//* Run SQANTI modules
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//****************************************************************************
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include { SQANTI_QC } from '../../../modules/local/cramino/cramino'
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include { SQANTI_FILTER } from '../../../modules/local/alfred/qc'
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include { SQANTI_RESCUE } from '../../../modules/local/alfred/qc'
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workflow BAM_QC {
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take:
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skip_sqanti_qc
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skip_sqanti_filter
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skip_sqanti_rescue
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reconstruction_program
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main:
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ch_versions = Channel.empty()
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// cramino
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if (skip_cramino != true) {
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CRAMINO( bam, cramino_min_length )
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ch_cramino = CRAMINO.out.cramino_stats
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ch_versions = ch_versions.mix(CRAMINO.out.versions.first())
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} else {
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ch_cramino = null
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}
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// alfred
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if (skip_alfred != true) {
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ALFRED( bam, genome_fasta )
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ch_alfred_stats = ALFRED.out.alfred_stats
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TRANSPOSE( ch_alfred_stats )
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ch_alfred_stats_transposed = TRANSPOSE.out.alfred_stats_transposed
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ch_versions = ch_versions.mix(ALFRED.out.versions.first())
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ch_versions = ch_versions.mix(TRANSPOSE.out.versions)
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} else {
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ch_alfred_stats = null
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ch_alfred_stats_transposed = null
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}
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// samtools flagstat
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if (skip_samtools_flagstat != true) {
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SAMTOOLS_FLAGSTAT( bam )
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ch_samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat
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ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)
50+
} else {
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ch_samtools_flagstat = null
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}
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54+
if (skip_ngs_bits != true) {
55+
NGS_BITS(
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mixed_bam,
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genome_fasta,
58+
ngs_bits_build,
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ngs_bits_skip_contamination
60+
)
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ch_ngs_bits = NGS_BITS.out.qcML
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ch_versions = ch_versions.mix(NGS_BITS.out.versions.first())
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} else {
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ch_ngs_bits = null
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}
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emit:
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cramino_stats = ch_cramino // channel: [ val(meta), [ bam ] ]
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alfred_stats = ch_alfred_stats // channel: [ val(meta), [ bai ] ]
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alfred_stats_transpose = ch_alfred_stats_transposed // channel: [ val(meta), [ bai ] ]
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flagstat = ch_samtools_flagstat // channel: [ val(meta), [ csi ] ]
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ngs_bits_stats = ch_ngs_bits
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versions = ch_versions // channel: [ versions.yml ]
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}

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