Skip to content

Commit

Permalink
Merge pull request #481 from nf-core/issue_477
Browse files Browse the repository at this point in the history 
Issue 477
  • Loading branch information
@nschcolnicov
nschcolnicov authored Nov 11, 2024
2 parents 3b7df98 + e32847c commit 4037e4c
Show file tree
Hide file tree
Showing 5 changed files with 64 additions and 42 deletions.
4 changes: 4 additions & 0 deletions CHANGELOG.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,10 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## Dev vTBD - TBD - TBD

- [[#477]](https://github.com/nf-core/smrnaseq/issues/481) - Fix [MIRTOP_STATS IndexError](https://github.com/nf-core/smrnaseq/issues/477) - Fix mirtop process execution when mirgenedb is used.

## v2.4.0 - 2024-10-14 - Navy Iron Boxer

- [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347) - change conda-base to conda-forge channel.
Expand Down
7 changes: 1 addition & 6 deletions subworkflows/local/mirna_quant.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,12 +94,7 @@ workflow MIRNA_QUANT {

ch_mirtop_logs = Channel.empty()

// nf-core/mirtop

ch_mirna_gtf_species = ch_mirna_gtf.map{ meta,gtf -> gtf }
.combine(ch_mirtrace_species)
.map{ gtf, species -> [ [id:species.toString()], gtf, species ] }
.collect()
ch_mirna_gtf_species = ch_mirna_gtf.map{ meta, gtf-> [ meta, gtf, meta.species ] }.collect()

BAM_STATS_MIRNA_MIRTOP(BOWTIE_MAP_SEQCLUSTER.out.bam, FORMAT_HAIRPIN.out.formatted_fasta, ch_mirna_gtf_species )

Expand Down
33 changes: 28 additions & 5 deletions subworkflows/local/prepare_genome/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,15 @@ workflow PREPARE_GENOME {
ch_mirtrace_species = val_mirtrace_species ? Channel.value(val_mirtrace_species) : Channel.empty()
mirna_gtf_from_species = val_mirtrace_species ? (val_mirtrace_species == 'hsa' ? "https://raw.githubusercontent.com/nf-core/test-datasets/smrnaseq/reference/hsa.gff3" : "https://mirbase.org/download/CURRENT/genomes/${val_mirtrace_species}.gff3") : false
ch_mirna_gtf = val_mirna_gtf ? Channel.fromPath(val_mirna_gtf, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : ( mirna_gtf_from_species ? Channel.fromPath(mirna_gtf_from_species, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() )

// Add species of the gtf in the meta
ch_mirna_gtf = ch_mirna_gtf
.combine(ch_mirtrace_species.ifEmpty('unknown'))
.map { meta, gtf, species ->
def new_meta = meta.clone() + [species: species]
[new_meta, gtf]
}

ch_mirna_adapters = params.with_umi ? [] : Channel.fromPath(val_fastp_known_mirna_adapters, checkIfExists: true).collect()

ch_rrna = val_rrna ? Channel.fromPath(val_rrna, checkIfExists: true).map{ it -> [ [id:'rRNA'], it ] }.collect() : Channel.empty()
Expand Down Expand Up @@ -118,15 +127,29 @@ workflow PREPARE_GENOME {

// Genome options
if (!params.mirgenedb) {
ch_reference_mature = params.mature ? Channel.fromPath(params.mature, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Mature miRNA fasta file not found: ${params.mature}" }
ch_reference_hairpin = params.hairpin ? Channel.fromPath(params.hairpin, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Hairpin miRNA fasta file not found: ${params.hairpin}" }
ch_reference_mature = params.mature ? Channel.fromPath(params.mature, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Specify a Mature miRNA fasta file via '--mature'" }
ch_reference_hairpin = params.hairpin ? Channel.fromPath(params.hairpin, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Specify a Hairpin miRNA fasta file via '--hairpin'" }
} else {
if (!params.mirgenedb_species) {
exit 1, "MirGeneDB species not set, please specify via the --mirgenedb_species parameter"
}
ch_reference_mature = params.mirgenedb_mature ? Channel.fromPath(params.mirgenedb_mature, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Mature miRNA fasta file not found via --mirgenedb_mature: ${params.mirgenedb_mature}" }
ch_reference_hairpin = params.mirgenedb_hairpin ? Channel.fromPath(params.mirgenedb_hairpin, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Hairpin miRNA fasta file not found via --mirgenedb_hairpin: ${params.mirgenedb_hairpin}" }
ch_mirna_gtf = params.mirgenedb_gff ? Channel.fromPath(params.mirgenedb_gff, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "MirGeneDB gff file not found via --mirgenedb_gff: ${params.mirgenedb_gff}"}
ch_reference_mature = params.mirgenedb_mature ? Channel.fromPath(params.mirgenedb_mature, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Specify a mirgenedb Mature miRNA fasta file via '--mirgenedb_mature'" }
ch_reference_hairpin = params.mirgenedb_hairpin ? Channel.fromPath(params.mirgenedb_hairpin, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Specify a mirgenedb Hairpin miRNA fasta file via '--mirgenedb_hairpin'" }
ch_mirna_gtf = params.mirgenedb_gff ? Channel.fromPath(params.mirgenedb_gff, checkIfExists: true).map{ it -> [ [id:it.baseName], it ] }.collect() : { exit 1, "Specify a MirGeneDB gff file via '--mirgenedb_gff'"}

// Create a channel for mirgenedb_species
ch_mirgenedb_species = Channel.value(params.mirgenedb_species)

// Add species of the gtf
// When mirgenedb workflow is not indicated, species defaults to val_mirtrace_species.
// If mirgenedb workflow parameters are indicated, the params.mirgenedb_species is used instead.
// If both mirgenedb workflow parameters and mirtrace_species (or mirna_gtf) are provided, params.mirgenedb_species is used as species value
ch_mirna_gtf = ch_mirna_gtf
.combine(ch_mirgenedb_species)
.map { meta, gtf, species ->
def new_meta = meta.clone() + [species: species]
[new_meta, gtf]
}
}

emit:
Expand Down
2 changes: 1 addition & 1 deletion tests/test_mirgenedb.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ nextflow_pipeline {
assertAll(
{ assert workflow.success },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert workflow.trace.succeeded().size() == 90 },
{ assert workflow.trace.succeeded().size() == 104 },
{ assert workflow.trace.failed().size() == 1 },

{ assert snapshot(
Expand Down
60 changes: 30 additions & 30 deletions tests/test_mirgenedb.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,31 +1,31 @@
{
"genome_quant_bam": {
"content": [
"Clone9_N1_mature_hairpin_genome.sorted.stats:md5,6b1d2b924593096358494dda37b46770",
"Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,aa37c5da7c2b4505ce58c3a21f97121c",
"Clone1_N1_mature_hairpin_genome.sorted.stats:md5,3c5f51cd7136eed5e97847ad7b857d23",
"Control_N1_mature_hairpin_genome.sorted.stats:md5,a7f2dd17a34c8f0b669a774404247394",
"Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,5bb521c495f1c450835299b1eb88dc84",
"Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,6a8ad3be2ca0fa924fd32a04293d4ce4",
"Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,d92f9eae7657418858e6d2b69436f74f",
"Control_N1_mature_hairpin_genome.sorted.idxstats:md5,a11f543771cea6b383fb596f60e998c3",
"Control_N1_mature_hairpin_genome.sorted.flagstat:md5,df2a57ac3b36f5d40793d3105a4bb2d1"
"Clone9_N1_mature_hairpin_genome.sorted.stats:md5,e81a1ccd658e49ae3e30a26f6d7ffa07",
"Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,8442f0f892abec766eb448b83311f46e",
"Clone1_N1_mature_hairpin_genome.sorted.stats:md5,951f3a5e3177dcba8aa264d8d5f6fa65",
"Control_N1_mature_hairpin_genome.sorted.stats:md5,d7d5f8f404858a052dc03b9b6f769248",
"Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,6971caaa71c465e63e844460f0a7d023",
"Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,82126b512243a091f7ddc94fa9dafb1d",
"Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,a2c5c718ff07f4bddcd216798b7c405a",
"Control_N1_mature_hairpin_genome.sorted.idxstats:md5,85d1e77dc9a3a0a3b173ba7db3fca34b",
"Control_N1_mature_hairpin_genome.sorted.flagstat:md5,81b7cd0fc5d8949a36089d2e6286338f"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-08T23:23:13.57712901"
"timestamp": "2024-11-11T13:44:14.743099344"
},
"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}, 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}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, 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_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
"{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}, CSVTK_JOIN={csvtk=0.30.0}, 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}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, 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_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-08T23:23:13.407922799"
"timestamp": "2024-11-11T13:44:14.583324793"
},
"mirna_quant_bam": {
"content": [
Expand All @@ -38,21 +38,21 @@
"Clone9_N1_mature.sorted.stats:md5,873e4f40e377cc445ace1ac48354729d",
"Control_N1_mature.sorted.idxstats:md5,b7a382b1d0f5cba6cb94b3b5a6b18f84",
true,
"Control_N1_mature_hairpin.sorted.idxstats:md5,79dc5e82ff88e7379c893549224cd87f",
"Control_N1_mature_hairpin.sorted.flagstat:md5,1dc7b98f0014a99a20de7c09a6b95340",
"Clone9_N1_mature_hairpin.sorted.idxstats:md5,f3ed5bf23f73d41c42d3da0bf30f89ea",
"Clone9_N1_mature_hairpin.sorted.stats:md5,c306ef4c5b1e23a3d032b532cf916fc1",
"Control_N1_mature_hairpin.sorted.idxstats:md5,25305882d997c5801388c5c881518296",
"Control_N1_mature_hairpin.sorted.flagstat:md5,569a6748d38176a240c351ba8b30eca8",
"Clone9_N1_mature_hairpin.sorted.idxstats:md5,265696d182c70f57bd7be26971def403",
"Clone9_N1_mature_hairpin.sorted.stats:md5,30266af34f3df2b8d807a1e620921ee6",
true,
true,
true,
"Control_N1_mature_hairpin.sorted.stats:md5,3e82fa30bfafcab2e8fb2f247e591959",
"Clone9_N1_mature_hairpin.sorted.flagstat:md5,678f4f9e98c3e1fcc5af54e8dd06fbbc"
"Control_N1_mature_hairpin.sorted.stats:md5,3bf3fdb23ef91c933887c71ad603999a",
"Clone9_N1_mature_hairpin.sorted.flagstat:md5,5729505d4df901b0c0cd93ab330526b5"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nextflow": "24.10.0"
},
"timestamp": "2024-10-08T23:23:13.503940378"
"timestamp": "2024-11-11T13:44:14.657194144"
},
"mirdeep2": {
"content": [
Expand Down Expand Up @@ -102,13 +102,13 @@
true,
"fastqc-1_sequence_counts_plot.txt:md5,59faee895ea86c12a4124d417e3bbd63",
"fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,0a4b4285f2c53dca216c107decc9921f",
"multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57",
"samtools-stats-dp.txt:md5,45c0315bade3f07942ded1ead37c1489",
"multiqc_citations.txt:md5,ea6d63393b7f47815a949fc58ee0caf8",
"samtools-stats-dp.txt:md5,c34196013e37d0c48671dbb70055c228",
"fastqc_sequence_length_distribution_plot.txt:md5,8b5cf1e3429a1ea0b3c63cfb176e1014",
"fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,a0502dd4f701c9deb646ffbec80c09de",
"fastqc-1_sequence_duplication_levels_plot.txt:md5,2072cda513c8884047d9d11c8aacbf33",
"fastqc-1_per_base_sequence_quality_plot.txt:md5,cafad80f4e07df53590cbabbbd024629",
"multiqc_general_stats.txt:md5,950d3fb06c211e984084e6de9dad6bb3",
"multiqc_general_stats.txt:md5,7064887136896292880f7ed09d256225",
"fastqc-1_per_base_n_content_plot.txt:md5,a0502dd4f701c9deb646ffbec80c09de",
"fastqc_per_base_n_content_plot.txt:md5,d907ac1ac9a4f19908b7b025eb75abfe",
"fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,0742b9813dcc95d4c62c52c83dec390c",
Expand All @@ -119,7 +119,7 @@
"fastqc-1-status-check-heatmap.txt:md5,d9c3ce24536a948e1fe9b84c55421ab7",
"fastqc_sequence_counts_plot.txt:md5,4861f0dc120e57e0359c53f417756b0c",
"fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,e9d8e3289f84f5a1ae6775813ec5a9b4",
"samtools_alignment_plot.txt:md5,b841ffce110bde994ccc6e977d2f856e",
"samtools_alignment_plot.txt:md5,3cc8b10a9d2a2317d7ac769d56bf5eb3",
"fastqc_per_base_sequence_quality_plot.txt:md5,a8adbff96d9adb317079e6becd7a80f6",
"fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,a0502dd4f701c9deb646ffbec80c09de",
"fastqc_adapter_content_plot.txt:md5,bd0fdc9c856c55598976b5a46c23a677",
Expand All @@ -133,10 +133,10 @@
"fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,585ec288b2514de54e8fb6251d1e0f98"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.0",
"nextflow": "24.10.0"
},
"timestamp": "2024-09-19T03:58:28.495279269"
"timestamp": "2024-11-11T13:44:14.815270775"
},
"multiqc": {
"content": [
Expand All @@ -148,4 +148,4 @@
},
"timestamp": "2024-08-30T20:30:51.144222162"
}
}
}

0 comments on commit 4037e4c

Please sign in to comment.