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Test dev #616

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Test dev #616

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10628e0
update container fusionreport
rannick Jan 20, 2025
2c59f51
fix path to process
rannick Jan 22, 2025
9b6cd24
Merge branch 'dev' into test-dev
rannick Feb 3, 2025
f7edce2
remove when usage, and double salmon dir
rannick Feb 13, 2025
571ec4b
Merge branch 'test-dev' of https://github.com/nf-core/rnafusion into …
rannick Feb 13, 2025
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8 changes: 2 additions & 6 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,6 @@ process {
}

withName: 'FUSIONREPORT' {
ext.when = { !params.skip_vis }
ext.args = { {params.no_cosmic} ? "--no-cosmic" : "" }
ext.args2 = "--export csv"
publishDir = [
Expand Down Expand Up @@ -211,7 +210,7 @@ process {

withName: 'SALMON_INDEX' {
publishDir = [
path: { "${params.genomes_base}/salmon" },
path: { "${params.genomes_base}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
Expand Down Expand Up @@ -360,7 +359,7 @@ process {
]
}

withName: 'NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
withName: 'NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
cpus = { 24 * task.attempt }
memory = { 100.GB * task.attempt }
time = { 2.d * task.attempt }
Expand All @@ -385,7 +384,4 @@ process {
ext.when = { {!params.fusioninspector_only} && {!params.skip_vcf} }
}

withName: '.*' {
ext.when = { !params.references_only || task.process.contains('BUILD_REFERENCES') }
}
}
5 changes: 1 addition & 4 deletions modules/local/fusioncatcher/build/main.nf
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Expand Up @@ -2,10 +2,7 @@ process FUSIONCATCHER_BUILD {
tag "fusioncatcher_build"
label 'process_medium'

conda "${projectDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
container "docker.io/clinicalgenomics/fusioncatcher:1.33"

input:
val genome_gencode_version
Expand Down
5 changes: 1 addition & 4 deletions modules/local/fusioncatcher/detect/main.nf
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Expand Up @@ -2,10 +2,7 @@ process FUSIONCATCHER_DETECT {
tag "$meta.id"
label 'process_high'

conda "${projectDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
container "docker.io/clinicalgenomics/fusioncatcher:1.33"

input:
tuple val(meta), path(fastqs, stageAs: "input/*")
Expand Down
4 changes: 2 additions & 2 deletions modules/local/gencode_download/main.nf
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Expand Up @@ -37,8 +37,8 @@ process GENCODE_DOWNLOAD {

stub:
"""
touch Homo_sapiens.${genome}.${genome_gencode_version}_dna_primary_assembly.fa
touch Homo_sapiens.${genome}.${genome_gencode_version}.gtf
touch Homo_sapiens_${genome}_${genome_gencode_version}_dna_primary_assembly.fa
touch Homo_sapiens_${genome}_${genome_gencode_version}.gtf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
7 changes: 4 additions & 3 deletions nextflow.config
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Expand Up @@ -11,6 +11,7 @@ params {

// Input options
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
outdir = null
references_only = false
cosmic_username = null
cosmic_passwd = null
Expand Down Expand Up @@ -77,7 +78,7 @@ params {
fai = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}_dna_primary_assembly.fa.fai"
gtf = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.gtf"
refflat = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.gtf.refflat"
rrna_intervals = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.interval_list"
rrna_intervals = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}.gtf.interval_list"
gencode_ref = "${params.genomes_base}/gencode"
no_cosmic = false
arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz"
Expand All @@ -87,14 +88,14 @@ params {
fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v${params.genome_gencode_version}"
hgnc_ref = "${params.genomes_base}/hgnc/hgnc_complete_set.txt"
hgnc_date = "${params.genomes_base}/hgnc/HGNC-DB-timestamp.txt"
salmon_index = "${params.genomes_base}/salmon/salmon"
salmon_index = "${params.genomes_base}/salmon"
starfusion_ref = "${params.genomes_base}/starfusion/ctat_genome_lib_build_dir"
starindex_ref = "${params.genomes_base}/star"
fusionreport_ref = "${params.genomes_base}/fusion_report_db"


// Internal file presence checks
salmon_index_stub_check = "${params.genomes_base}/salmon/salmon/complete_ref_lens.bin"
salmon_index_stub_check = "${params.genomes_base}/salmon/complete_ref_lens.bin"
starindex_ref_stub_check = "${params.genomes_base}/star/star/Genome"
fusionreport_ref_stub_check = "${params.genomes_base}/fusion_report_db/mitelman.db"
fusioncatcher_ref_stub_check = "${params.genomes_base}/fusioncatcher/human_v${params.genome_gencode_version}/ensembl_fully_overlapping_genes.txt"
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/build_references.nf
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Expand Up @@ -87,7 +87,7 @@ workflow BUILD_REFERENCES {
}

if (!file(params.salmon_index).exists() || file(params.salmon_index).isEmpty() ||
!file(params.salmon_index_stub_check).exists() || file(params.salmon_index_stub_check).isEmpty()){ // add condition for qc
!file(params.salmon_index_stub_check).exists() || file(params.salmon_index_stub_check).isEmpty()){
GFFREAD(ch_gtf, ch_fasta.map{ it -> it[1] })
ch_versions = ch_versions.mix(GFFREAD.out.versions)
SALMON_INDEX(ch_fasta.map{ it -> it[1] }, GFFREAD.out.gffread_fasta.map{ it -> it[1] })
Expand Down Expand Up @@ -149,7 +149,7 @@ workflow BUILD_REFERENCES {
}


if ((params.fusionreport || params.all) &&
if ((params.fusionreport || params.all || params.fusioncatcher || params.arriba || params.starfusion) &&
(!file(params.fusionreport_ref).exists() || file(params.fusionreport_ref).isEmpty() ||
!file(params.fusionreport_ref_stub_check).exists() || file(params.fusionreport_ref_stub_check).isEmpty())) {
if (!params.no_cosmic && (!params.cosmic_username || !params.cosmic_passwd)) { exit 1, 'COSMIC username and/or password missing' }
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/fusioncatcher_workflow/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ workflow FUSIONCATCHER_WORKFLOW {
take:
reads // channel [ meta, [ fastqs ] ]
fusioncatcher_ref // channel [ meta, path ]
run_fusioncatcher // boolean
fusioncatcher // boolean
all // boolean
fusioninspector_only // boolean
fusioncatcher_fusions // path, string
Expand All @@ -18,7 +18,7 @@ workflow FUSIONCATCHER_WORKFLOW {
ch_versions = Channel.empty()
ch_dummy_file = file("$baseDir/assets/dummy_file_fusioncatcher.txt", checkIfExists: true)

if (( run_fusioncatcher || all) && !fusioninspector_only ) {
if (( fusioncatcher || all) && !fusioninspector_only ) {
if (fusioncatcher_fusions){

ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true)))
Expand Down
1 change: 0 additions & 1 deletion subworkflows/local/fusionreport_workflow/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@ workflow FUSIONREPORT_WORKFLOW {
ch_versions = Channel.empty()
ch_report = Channel.empty()
ch_csv = Channel.empty()

if (!params.fusioninspector_only) {
reads_fusions = reads
.join(arriba_fusions, failOnMismatch:true, failOnDuplicate:true)
Expand Down
99 changes: 50 additions & 49 deletions workflows/rnafusion.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ workflow RNAFUSION {
BUILD_REFERENCES()
ch_versions = ch_versions.mix(BUILD_REFERENCES.out.versions)

if (!params.references_only) { // TODO: Remove this temporary parameter when we have a full-working GitHub nf-test
if (!params.references_only) {

//
// QC from FASTQ files
Expand Down Expand Up @@ -118,16 +118,16 @@ workflow RNAFUSION {



//Run fusioncatcher
FUSIONCATCHER_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusioncatcher_ref, // channel [ meta, path ]
params.run_fusioncatcher,
params.all,
params.fusioninspector_only,
params.fusioncatcher_fusions
)
ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions)
//Run fusioncatcher
FUSIONCATCHER_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusioncatcher_ref, // channel [ meta, path ]
params.fusioncatcher,
params.all,
params.fusioninspector_only,
params.fusioncatcher_fusions
)
ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions)


//Run stringtie
Expand All @@ -139,31 +139,35 @@ workflow RNAFUSION {


//Run fusion-report
FUSIONREPORT_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusionreport_ref,
ARRIBA_WORKFLOW.out.fusions,
STARFUSION_WORKFLOW.out.fusions,
FUSIONCATCHER_WORKFLOW.out.fusions
)
ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions)
if (params.fusioncatcher || params.starfusion || params.arriba || params.all) {
FUSIONREPORT_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusionreport_ref,
ARRIBA_WORKFLOW.out.fusions,
STARFUSION_WORKFLOW.out.fusions,
FUSIONCATCHER_WORKFLOW.out.fusions
)
ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions)
}

//Run fusionInpector
FUSIONINSPECTOR_WORKFLOW (
ch_reads,
FUSIONREPORT_WORKFLOW.out.fusion_list,
FUSIONREPORT_WORKFLOW.out.fusion_list_filtered,
FUSIONREPORT_WORKFLOW.out.report,
FUSIONREPORT_WORKFLOW.out.csv,
STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed,
BUILD_REFERENCES.out.ch_gtf,
BUILD_REFERENCES.out.ch_arriba_ref_protein_domains,
BUILD_REFERENCES.out.ch_arriba_ref_cytobands,
BUILD_REFERENCES.out.ch_hgnc_ref,
BUILD_REFERENCES.out.ch_hgnc_date
)
ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions)

if (params.fusioncatcher || params.starfusion || params.arriba || params.all) {
FUSIONINSPECTOR_WORKFLOW (
ch_reads,
FUSIONREPORT_WORKFLOW.out.fusion_list,
FUSIONREPORT_WORKFLOW.out.fusion_list_filtered,
FUSIONREPORT_WORKFLOW.out.report,
FUSIONREPORT_WORKFLOW.out.csv,
STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed,
BUILD_REFERENCES.out.ch_gtf,
BUILD_REFERENCES.out.ch_arriba_ref_protein_domains,
BUILD_REFERENCES.out.ch_arriba_ref_cytobands,
BUILD_REFERENCES.out.ch_hgnc_ref,
BUILD_REFERENCES.out.ch_hgnc_date
)
ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.ch_arriba_visualisation.collect{it[1]}.ifEmpty([]))
ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions)
}

//QC
QC_WORKFLOW (
Expand All @@ -175,7 +179,19 @@ workflow RNAFUSION {
)
ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions)


ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_html.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_json.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastqc_trimmed.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_gene_count.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([]))

}

//
// Collate and save software versions
//
Expand Down Expand Up @@ -219,19 +235,6 @@ workflow RNAFUSION {
)
)

if (!params.references_only) { // TODO: Remove this temporary parameter when we have a full-working GitHub nf-test
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_html.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_json.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastqc_trimmed.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_gene_count.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.ch_arriba_visualisation.collect{it[1]}.ifEmpty([]))
}

MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
Expand All @@ -241,8 +244,6 @@ workflow RNAFUSION {
[]
)



emit:
multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
versions = ch_versions // channel: [ path(versions.yml) ]
Expand Down
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