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Addressing PR comments
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zxBIB Schcolnicov committed Sep 30, 2024
1 parent 97c01bc commit 8e54dbc
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Showing 8 changed files with 14 additions and 14 deletions.
2 changes: 1 addition & 1 deletion subworkflows/local/genome_quant.nf
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Expand Up @@ -7,7 +7,7 @@ include { BOWTIE_ALIGN as BOWTIE_MAP_GENOME } from '../../modules/nf-core/bowtie

workflow GENOME_QUANT {
take:
ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ]
ch_bowtie_index // channel: [ val(meta), [ path(directory_index) ] ]
ch_fasta // channel: [ val(meta), path(fasta) ]
ch_reads // channel: [ val(meta), [ reads ] ]

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6 changes: 3 additions & 3 deletions subworkflows/local/prepare_genome/main.nf
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Expand Up @@ -27,7 +27,7 @@ workflow PREPARE_GENOME {

// Parameter channel handling
ch_fasta = val_fasta ? Channel.fromPath(val_fasta, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()
ch_bowtie_index = val_bowtie_index ? Channel.fromPath(val_bowtie_index, checkIfExists: true).map{ it -> [ [id:'bowtie_index'], it ] }.collect() : Channel.empty()
ch_bowtie_index = val_bowtie_index ? Channel.fromPath(val_bowtie_index, checkIfExists: true).map{ it -> [ [], it ] }.collect() : Channel.empty()

bool_mirtrace_species = val_mirtrace_species ? true : false
bool_has_fasta = val_fasta ? true : false
Expand Down Expand Up @@ -55,7 +55,7 @@ workflow PREPARE_GENOME {
ch_bowtie_index = UNTAR_BOWTIE_INDEX.out.files
ch_versions = ch_versions.mix(UNTAR_BOWTIE_INDEX.out.versions)
} else {
ch_bowtie_index = Channel.fromPath("${val_bowtie_index}**ebwt", checkIfExists: true).map{it -> [ [id:'bowtie_index'], it ] }.collect()
ch_bowtie_index = Channel.fromPath("${val_bowtie_index}**ebwt", checkIfExists: true).map{it -> [ [id:it.baseName], it ] }.collect()
.ifEmpty{ error "Bowtie1 index directory not found: ${val_bowtie_index}" }
.filter { it != null }
}
Expand Down Expand Up @@ -96,7 +96,7 @@ workflow PREPARE_GENOME {
emit:
fasta = ch_fasta // channel: [ val(meta), path(fasta) ]
has_fasta = bool_has_fasta // boolean
bowtie_index = ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ]
bowtie_index = ch_bowtie_index // channel: [ val(meta), [ path(directory_index) ] ]
versions = ch_versions // channel: [ versions.yml ]
mirtrace_species = ch_mirtrace_species // channel: [ val(string) ]
has_mirtrace_species = bool_mirtrace_species // boolean
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/fastq_find_mirna_mirdeep2/main.nf
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4 changes: 2 additions & 2 deletions tests/test_contamination_tech_reps.nf.test.snap
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Expand Up @@ -34,13 +34,13 @@
},
"software_versions": {
"content": [
"{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, DATATABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
"{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-26T00:13:46.736133"
"timestamp": "2024-09-30T15:53:12.532061"
},
"mirna_quant_bam": {
"content": [
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4 changes: 2 additions & 2 deletions tests/test_nextflex.nf.test.snap
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Expand Up @@ -34,13 +34,13 @@
},
"software_versions": {
"content": [
"{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, DATATABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
"{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-26T00:29:08.657006"
"timestamp": "2024-09-30T16:10:06.50556"
},
"mirna_quant_bam": {
"content": [
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4 changes: 2 additions & 2 deletions tests/test_skipfastp.nf.test.snap
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Expand Up @@ -41,13 +41,13 @@
},
"software_versions": {
"content": [
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, DATATABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-26T00:53:04.938088"
"timestamp": "2024-09-30T16:13:51.93255"
},
"mirna_quant_bam": {
"content": [
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4 changes: 2 additions & 2 deletions tests/test_umi.nf.test.snap
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Expand Up @@ -41,13 +41,13 @@
},
"software_versions": {
"content": [
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, DATATABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
"{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-26T01:02:56.214416"
"timestamp": "2024-09-30T16:23:12.559357"
},
"mirna_quant_bam": {
"content": [
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2 changes: 1 addition & 1 deletion workflows/smrnaseq.nf
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Expand Up @@ -53,7 +53,7 @@ workflow NFCORE_SMRNASEQ {
ch_reference_hairpin // channel: [ val(meta), path(fasta) ]
ch_mirna_gtf // channel: [ val(meta), path(gtf) ]
ch_fasta // channel: [ val(meta), path(fasta) ]
ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ]
ch_bowtie_index // channel: [ val(meta), [ path(directory_index) ] ]
ch_rrna // channel: [ val(meta), path(fasta) ]
ch_trna // channel: [ val(meta), path(fasta) ]
ch_cdna // channel: [ val(meta), path(fasta) ]
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