mirror of
https://github.com/MillironX/nf-core_modules.git
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e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
108 lines
4.2 KiB
YAML
108 lines
4.2 KiB
YAML
- name: fastp test_fastp_single_end
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
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- "single end (151 cycles)"
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- path: output/fastp/test.fastp.log
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contains:
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- "Q20 bases: 12922(92.9841%)"
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- "reads passed filter: 99"
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- path: output/fastp/test.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.json
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md5sum: a517ba37b17a342b5428f2c1f8fe3dd7
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- name: fastp test_fastp_paired_end
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
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- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
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- path: output/fastp/test.fastp.log
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contains:
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- "No adapter detected for read1"
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- "Q30 bases: 12281(88.3716%)"
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test_1.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test_2.trim.fastq.gz
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md5sum: 532b190fb4dc7b2277ee5cf1464e598c
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- name: fastp test_fastp_single_end_trim_fail
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
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- "single end (151 cycles)"
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- path: output/fastp/test.fastp.log
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contains:
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- "Q20 bases: 12922(92.9841%)"
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- "reads passed filter: 99"
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- path: output/fastp/test.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test.fastp.json
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md5sum: 4be682c727942a45fc4c8600c28694a8
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- path: output/fastp/test.fail.fastq.gz
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md5sum: b57f2026eb259a0b0c0b3960c270258d
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- name: fastp test_fastp_paired_end_trim_fail
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
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- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
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- path: output/fastp/test.fastp.log
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contains:
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- "No adapter detected for read1"
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- "Q30 bases: 12281(88.3716%)"
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test_1.trim.fastq.gz
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md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
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- path: output/fastp/test_2.trim.fastq.gz
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md5sum: 532b190fb4dc7b2277ee5cf1464e598c
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- path: output/fastp/test_1.fail.fastq.gz
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/fastp/test_2.fail.fastq.gz
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md5sum: 72d0002841967676ac936d08746a9128
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- name: fastp test_fastp_paired_end_merged
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "<div id='After_filtering__merged__quality'>"
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- path: output/fastp/test.fastp.json
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contains:
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- '"merged_and_filtered": {'
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- '"total_reads": 75'
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- '"total_bases": 13683'
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- path: output/fastp/test.fastp.log
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contains:
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- "Merged and filtered:"
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- "total reads: 75"
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- "total bases: 13683"
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- path: output/fastp/test.merged.fastq.gz
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md5sum: 4955ca2c899729b17bd526d2626a8d73
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- path: output/fastp/test_1.trim.fastq.gz
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md5sum: 4a03721ee252b7c6e81e007550e6ab63
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- path: output/fastp/test_2.trim.fastq.gz
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md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace
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