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Add nf-test for local module blat_mirna
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a80e451
add test for blat mirna
atrigila 613ba65
add small test with contamination filter
atrigila 13ab7bf
Merge branch 'dev' into nf_tests_blat
atrigila 13d77c5
update changelog
atrigila c425db9
Merge branch 'nf_tests_blat' of https://github.com/atrigila/smrnaseq …
atrigila f525be2
Merge branch 'dev' into nf_tests_blat
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
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| Use as follows: | ||
| nextflow run nf-core/smrnaseq -profile test_contamination,<docker/singularity> --outdir <OUTDIR> | ||
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| ---------------------------------------------------------------------------------------- | ||
| */ | ||
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| params { | ||
| config_profile_name = 'Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function with contamination filter' | ||
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| // Limit resources so that this can run on GitHub Actions | ||
| max_cpus = 2 | ||
| max_memory = '6.GB' | ||
| max_time = '6.h' | ||
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| // Input data | ||
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| input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv' | ||
| fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa' | ||
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| mirtrace_species = 'hsa' | ||
| skip_mirdeep = true | ||
| save_merged = false | ||
| save_aligned_mirna_quant = false | ||
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| filter_contamination = true | ||
| cdna = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.cdna.all.fa" | ||
| ncrna = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.ncrna.fa" | ||
| trna = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/hg19-tRNAs.fa" | ||
| } | ||
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| // Include illumina config to run test without additional profiles | ||
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| includeConfig 'protocol_illumina.config' | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| process BLAT_MIRNA { | ||
| tag "$fasta" | ||
| label 'process_medium' | ||
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| conda 'bioconda::blat=36' | ||
| container 'community.wave.seqera.io/library/ucsc-blat:445--32730933d3c2c916' | ||
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| input: | ||
| val db_type | ||
| path mirna | ||
| path contaminants | ||
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| output: | ||
| path 'filtered.fa' , emit: filtered_set | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| if ( db_type == "cdna" ) | ||
| """ | ||
| echo $db_type | ||
| awk '/^>/ { x=index(\$6, "transcript_biotype:miRNA") } { if(!x) print }' $contaminants > subset.fa | ||
| blat -out=blast8 $mirna subset.fa /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' subset.fa > filtered.fa | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
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| else if ( db_type == "ncrna" ) | ||
| """ | ||
| echo $db_type | ||
| awk '/^>/ { x=(index(\$6, "transcript_biotype:rRNA") || index(\$6, "transcript_biotype:miRNA")) } { if(!x) print }' $contaminants > subset.fa | ||
| blat -out=blast8 $mirna subset.fa /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' subset.fa > filtered.fa | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
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| else | ||
| """ | ||
| echo $db_type | ||
| blat -out=blast8 $mirna $contaminants /dev/stdout | awk 'BEGIN{FS="\t"}{if(\$11 < 1e-5)print \$1;}' | uniq > mirnahit.txt | ||
| awk 'BEGIN { while((getline<"mirnahit.txt")>0) l[">"\$1]=1 } /^>/ {x = l[\$1]} {if(!x) print }' $contaminants > filtered.fa | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| blat: \$(echo \$(blat) | grep Standalone | awk '{ if (match(\$0,/[0-9]*[0-9]/,m)) print m[0] }') | ||
| END_VERSIONS | ||
| """ | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| nextflow_process { | ||
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| name "Test Process BLAT_MIRNA" | ||
| script "../blat_mirna.nf" | ||
| process "BLAT_MIRNA" | ||
| tag "modules" | ||
| tag "modules_local" | ||
| tag "blat_mirna" | ||
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| test("cDNA BLAT - Human") { | ||
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| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = "cdna" | ||
| input[1] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa", checkIfExists: true)] | ||
| input[2] = [file("https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.cdna.all.fa", checkIfExists: true)] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
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| with(process.out.filtered_set) { | ||
| with(get(0)) { | ||
| assert get(0).endsWith("filtered.fa") | ||
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| // Check for AWK filtering of specific biotype | ||
| def lines = path(get(0)).readLines() | ||
| assert !lines.any { it.contains("transcript_biotype:miRNA") } | ||
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| // Check for exclusion of miRNAs hits | ||
| assert !lines.any { it.contains("ENST00000564740.1") } | ||
| } | ||
| } | ||
| } | ||
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| } | ||
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| test("ncRNA BLAT - Human") { | ||
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| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = "ncRNA" | ||
| input[1] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa", checkIfExists: true)] | ||
| input[2] = [file("https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.ncrna.fa", checkIfExists: true)] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
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| with(process.out.filtered_set) { | ||
| with(get(0)) { | ||
| assert get(0).endsWith("filtered.fa") | ||
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| // Check for AWK filtering of specific biotype | ||
| def lines = path(get(0)).readLines() | ||
| // Lines contain transcript_biotype:rRNA or miRNA, so AWK assertions do not work: | ||
| //assert !lines.any { it.contains("transcript_biotype:rRNA") } | ||
| //assert !lines.any { it.contains("transcript_biotype:miRNA") } | ||
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| // Check for exclusion of miRNAs hits | ||
| assert !lines.any { it.contains("ENST00000564740.1") } | ||
| } | ||
| } | ||
| } | ||
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| } | ||
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| test("tRNA BLAT - Human") { | ||
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| when { | ||
| params { | ||
| outdir = "${outputDir}" | ||
| } | ||
| process { | ||
| """ | ||
| input[0] = "tRNA" | ||
| input[1] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa", checkIfExists: true)] | ||
| input[2] = [file("https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/hg19-tRNAs.fa", checkIfExists: true)] | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assert process.success | ||
| assert snapshot(process.out).match() | ||
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| with(process.out.filtered_set) { | ||
| with(get(0)) { | ||
| assert get(0).endsWith("filtered.fa") | ||
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| // Check for exclusion of miRNAs hits | ||
| def lines = path(get(0)).readLines() | ||
| assert !lines.any { it.contains("ENST00000564740.1") } | ||
| } | ||
| } | ||
| } | ||
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| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| { | ||
| "ncRNA BLAT - Human": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| "filtered.fa:md5,6bc8a430400e2e78cf7f474981230811" | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ], | ||
| "filtered_set": [ | ||
| "filtered.fa:md5,6bc8a430400e2e78cf7f474981230811" | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-23T17:53:35.313580289" | ||
| }, | ||
| "tRNA BLAT - Human": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| "filtered.fa:md5,6b54e95ca5418d7d9c4d331ca3b2c96f" | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ], | ||
| "filtered_set": [ | ||
| "filtered.fa:md5,6b54e95ca5418d7d9c4d331ca3b2c96f" | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-23T17:57:58.238216453" | ||
| }, | ||
| "cDNA BLAT - Human": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| "filtered.fa:md5,8fd42894e815999b4278b08297720aae" | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ], | ||
| "filtered_set": [ | ||
| "filtered.fa:md5,8fd42894e815999b4278b08297720aae" | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e2957df2cc8f0410101564c8e65d1761" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-23T17:53:16.735132971" | ||
| } | ||
| } |
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This test profile is almost identical to test_full_filter_contamination isn't it?
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Yes! The input samplesheet is smaller, though