From a9e10a9e2479baa48a6d77341d83d79708bbe1b7 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 24 Mar 2023 12:10:58 +0000 Subject: [PATCH 1/3] Changes to pep file naming and mem for some jobs --- conf/base.config | 6 +++--- subworkflows/local/pep_alignments.nf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/base.config b/conf/base.config index 8c59de83..6f9c3f62 100644 --- a/conf/base.config +++ b/conf/base.config @@ -23,14 +23,14 @@ process { // RESOURCES: MEMORY INTENSIVE STEPS, SOFTWARE TO BE UPDATED TO COMBAT THIS withName: '.*:.*:SELFCOMP:(SELFCOMP_ALIGNMENTBLOCKS|SELFCOMP_MAPIDS|SELFCOMP_MUMMER2BED|SELFCOMP_SPLITFASTA|BEDTOOLS_MERGE)' { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 80.GB * task.attempt, 'memory') } + cpus = { check_max( 10 * task.attempt, 'cpus' ) } + memory = { check_max( 100.GB * task.attempt, 'memory') } time = { check_max( 8.h * task.attempt, 'time' ) } } // RESOURCES: CHANGES TO FREQUENT FAILURES BELOW THIS MEM POINT withName: '(MINIPROT_ALIGN|MINIMAP2_ALIGN)' { - memory = { check_max( 50.GB * task.attempt, 'memory' ) } + memory = { check_max( 100.GB * task.attempt, 'memory' ) } } // 25GB * (task attempt * 2) = 50GB, 100GB, 150GB diff --git a/subworkflows/local/pep_alignments.nf b/subworkflows/local/pep_alignments.nf index 5a990257..24a48ee8 100644 --- a/subworkflows/local/pep_alignments.nf +++ b/subworkflows/local/pep_alignments.nf @@ -53,7 +53,7 @@ workflow PEP_ALIGNMENTS { // MINIPROT_ALIGN.out.gff .map { it -> - tuple([ id: it[0].org, + tuple([ id: it[0].org + '_pep', type: it[0].type ], it[1] ) From 3d92489b8b5d926e3d6ac8681e0f0b1f9ca4963e Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 24 Mar 2023 15:06:55 +0000 Subject: [PATCH 2/3] Updates to get rid of multiple samtools faidx runs --- subworkflows/local/gene_alignment.nf | 4 ++++ subworkflows/local/generate_genome.nf | 1 + subworkflows/local/nuc_alignments.nf | 10 ++-------- workflows/treeval.nf | 1 + 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/gene_alignment.nf b/subworkflows/local/gene_alignment.nf index 8c8140d0..736a3310 100644 --- a/subworkflows/local/gene_alignment.nf +++ b/subworkflows/local/gene_alignment.nf @@ -17,6 +17,7 @@ workflow GENE_ALIGNMENT { take: dot_genome // Channel: [val(meta), [ datafile ]] reference_tuple + reference_index assembly_classT alignment_datadir alignment_genesets @@ -78,16 +79,19 @@ workflow GENE_ALIGNMENT { // SUBWORKFLOW: GENERATES GENE ALIGNMENTS FOR RNA, NUCLEAR AND COMPLEMENT_DNA DATA, EMITS BIGBED // GEN_ALIGNMENTS ( reference_tuple, + reference_index, gen_files, dot_genome, intron_size ) CDS_ALIGNMENTS ( reference_tuple, + reference_index, cds_files, dot_genome, intron_size ) RNA_ALIGNMENTS ( reference_tuple, + reference_index, rna_files, dot_genome, intron_size ) diff --git a/subworkflows/local/generate_genome.nf b/subworkflows/local/generate_genome.nf index 0c568ca9..370fc31f 100644 --- a/subworkflows/local/generate_genome.nf +++ b/subworkflows/local/generate_genome.nf @@ -34,6 +34,7 @@ workflow GENERATE_GENOME { emit: dot_genome = GENERATE_GENOME_FILE.out.dotgenome + ref_index = SAMTOOLS_FAIDX.out.fai reference_tuple = to_samtools versions = ch_versions.ifEmpty(null) diff --git a/subworkflows/local/nuc_alignments.nf b/subworkflows/local/nuc_alignments.nf index 7f6c7d16..eebe4af5 100644 --- a/subworkflows/local/nuc_alignments.nf +++ b/subworkflows/local/nuc_alignments.nf @@ -9,6 +9,7 @@ include { UCSC_BEDTOBIGBED } from '../../modules/nf-core/ucsc/bedtobigbed/m workflow NUC_ALIGNMENTS { take: reference_tuple + reference_index nuc_files dot_genome intron_size @@ -41,13 +42,6 @@ workflow NUC_ALIGNMENTS { ) .set { formatted_input } - // - // MODULE: GENERATES FASTA INDEX OF REFERENCE - // EMITS FAIDX FILE - // - SAMTOOLS_FAIDX ( reference_tuple ) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - // // MODULE: ALIGNS REFERENCE FAIDX TO THE GENE_ALIGNMENT QUERY FILE FROM NUC_FILES // EMITS ALIGNED BAM FILE @@ -71,7 +65,7 @@ workflow NUC_ALIGNMENTS { tuple([id: meta.org, type: meta.type], file) } .groupTuple( by: [0] ) .combine( reference_tuple ) - .combine( SAMTOOLS_FAIDX.out.fai ) + .combine( reference_index ) .multiMap { it -> nuc_grouped: tuple( it[0], it[1] ) reference: it[-3] diff --git a/workflows/treeval.nf b/workflows/treeval.nf index 4fb42f92..686a519e 100644 --- a/workflows/treeval.nf +++ b/workflows/treeval.nf @@ -101,6 +101,7 @@ workflow TREEVAL { // GENE_ALIGNMENT ( GENERATE_GENOME.out.dot_genome, GENERATE_GENOME.out.reference_tuple, + GENERATE_GENOME.out.ref_index, YAML_INPUT.out.assembly_classT, YAML_INPUT.out.align_data_dir, YAML_INPUT.out.align_geneset, From 13388f0911ced93c2e3993b665aaefac3849b12e Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 24 Mar 2023 18:38:24 +0000 Subject: [PATCH 3/3] Added a missing versions statement --- subworkflows/local/nuc_alignments.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/nuc_alignments.nf b/subworkflows/local/nuc_alignments.nf index eebe4af5..08625569 100644 --- a/subworkflows/local/nuc_alignments.nf +++ b/subworkflows/local/nuc_alignments.nf @@ -87,6 +87,7 @@ workflow NUC_ALIGNMENTS { // MODULE: CONVERTS THE ABOVE MERGED BAM INTO BED FORMAT // BEDTOOLS_BAMTOBED { SAMTOOLS_MERGE.out.bam } + ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions) // // MODULE: SORTS THE ABOVE BED FILE