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Issue 477 #481

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merged 4 commits into from
Nov 11, 2024
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Merged

Issue 477 #481

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e89826f
add species to gtf meta
atrigila Nov 5, 2024
8e1846a
Update CHANGELOG, remove dumps, update error message for reference fi…
nschcolnicov Nov 11, 2024
c8ae4c6
Minor fixes
nschcolnicov Nov 11, 2024
e32847c
Updated changelog
nschcolnicov Nov 11, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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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.
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7 changes: 1 addition & 6 deletions subworkflows/local/mirna_quant.nf
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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 )

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33 changes: 28 additions & 5 deletions subworkflows/local/prepare_genome/main.nf
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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
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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
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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"
}
}
}
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