nf-core_modules/tests/modules/fastp/test.yml

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- name: fastp test_fastp_single_end
command: nextflow run tests/modules/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
2021-02-01 13:02:06 +00:00
tags:
- fastp
2021-02-01 13:02:06 +00:00
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "single end (151 cycles)"
- path: output/fastp/test.fastp.log
contains:
- "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00
md5sum: e2257263668dc8a75d95475099fb472d
- path: output/fastp/test.fastp.json
md5sum: e0d856ebb3da9e4462c3ce9683efe01d
2021-02-01 13:02:06 +00:00
- name: fastp test_fastp_paired_end
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
2021-02-01 13:02:06 +00:00
tags:
- fastp
2021-02-01 13:02:06 +00:00
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
- path: output/fastp/test.fastp.log
contains:
- "No adapter detected for read1"
- "Q30 bases: 12281(88.3716%)"
- path: output/fastp/test.fastp.json
contains:
- '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00
md5sum: e2257263668dc8a75d95475099fb472d
- path: output/fastp/test_2.trim.fastq.gz
Converge test data usage (#249) * initial data restructuing * fixed bedtools_complement * fixed bedtools_genomecov * fixed bedtools_getfasta * fixed bedtools_intersect * fixed bedtools maskfasta * fixed bedtools_merge * fixed bedtools_slop * fixed bedtools_sort * fixed bismark_genome_preparation * fixed blast * fixed bowtie data * fixed bowtie2 data * fixed bwa data * fixed bwamem2 data usage * fixed cat_fastq data * fixed cutadapt data * fixed dsh data * fixed fastp data * fixed fastqc; fixed bug with wrong fastq format * fixed gatk * fixed data for gffread, gunzip * fixed ivar paths * fixed data paths for minimap2 * fixed mosdepth * fixed multiqc, pangolin * fixed picard data paths * fixed data paths for qualimap, quast * fixed salmon data paths * fixed samtools paths * fixed seqwish, stringtie paths * fixed tabix, trimgalore paths * cleaned up data * added first description to README * changed test data naming again; everything up to bwa fixed * everything up to gatk4 * fixed everything up to ivar * fixed everything up to picard * everything up to quast * everything fixed up to stringtie * switched everyting to 'test' naming scheme * fixed samtools and ivar tests * cleaned up README a bit * add (simulated) methylation test data based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90 * bwameth/align: update data paths and checksums also, build index on the go * bwameth/index: update data paths and checksums * methyldackel/extract: update data paths and checksums * methyldackel/mbias: update data paths and checksums * bismark/deduplicate: update data paths and checksums * remove obsolete testdata * remove empty 'dummy_file.txt' * update data/README.md * methyldackel: fix test * Revert "methyldackel: fix test" This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a. * methyldackel: fix test for real * move test.genome.sizes * changed test names * switched genomic to genome and transcriptome * fix bedtools, blast * fix gtf, tabix, .paf * fix bowtie,bwa,bwameth * fixed: bwa, bwamem, gatk, gffread, quast * fixed bismark and blast * fixed remaining tests * delete bam file Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00
md5sum: 9eff7203596580cc5e42aceab4a469df
- name: fastp test_fastp_single_end_trim_fail
command: nextflow run tests/modules/fastp -entry test_fastp_single_end_trim_fail -c tests/config/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "single end (151 cycles)"
- path: output/fastp/test.fastp.log
contains:
- "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d
- path: output/fastp/test.fastp.json
md5sum: ee65a46d6e59fa556f112727b8a902ce
- path: output/fastp/test.fail.fastq.gz
md5sum: de315d397c994d8e66bafc7a8dc11070
- name: fastp test_fastp_paired_end_trim_fail
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c tests/config/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
- path: output/fastp/test.fastp.log
contains:
- "No adapter detected for read1"
- "Q30 bases: 12281(88.3716%)"
- path: output/fastp/test.fastp.json
contains:
- '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d
- path: output/fastp/test_2.trim.fastq.gz
md5sum: 9eff7203596580cc5e42aceab4a469df
- path: output/fastp/test_1.fail.fastq.gz
md5sum: e62ff0123a74adfc6903d59a449cbdb0
- path: output/fastp/test_2.fail.fastq.gz
md5sum: f52309b35a7c15cbd56a9c3906ef98a5
- name: fastp test_fastp_paired_end_merged
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_merged -c tests/config/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "<div id='After_filtering__merged__quality'>"
- path: output/fastp/test.fastp.json
contains:
- '"merged_and_filtered": {'
- '"total_reads": 75'
- '"total_bases": 13683'
- path: output/fastp/test.fastp.log
contains:
- "Merged and filtered:"
- "total reads: 75"
- "total bases: 13683"
- path: output/fastp/test.merged.fastq.gz
md5sum: ce88539076ced5aff11f866836ea1f40
- path: output/fastp/test_1.trim.fastq.gz
md5sum: 65d75c13abbfbfd993914e1379634100
- path: output/fastp/test_2.trim.fastq.gz
md5sum: 0d87ce4d8ef29fb35f337eb0f6c9fcb4