2021-03-24 12:08:59 -04:00
|
|
|
- name: fastp test_fastp_single_end
|
2021-07-07 05:10:18 -04:00
|
|
|
command: nextflow run tests/modules/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
|
2021-02-01 08:02:06 -05:00
|
|
|
tags:
|
2021-03-24 12:08:59 -04:00
|
|
|
- fastp
|
2021-02-01 08:02:06 -05:00
|
|
|
files:
|
2021-03-24 12:08:59 -04:00
|
|
|
- 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 05:10:57 -05:00
|
|
|
md5sum: e2257263668dc8a75d95475099fb472d
|
2021-03-24 12:08:59 -04:00
|
|
|
- path: output/fastp/test.fastp.json
|
|
|
|
|
md5sum: e0d856ebb3da9e4462c3ce9683efe01d
|
2021-02-01 08:02:06 -05:00
|
|
|
|
2021-03-24 12:08:59 -04:00
|
|
|
- name: fastp test_fastp_paired_end
|
2021-07-07 05:10:18 -04:00
|
|
|
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
|
2021-02-01 08:02:06 -05:00
|
|
|
tags:
|
2021-03-24 12:08:59 -04:00
|
|
|
- fastp
|
2021-02-01 08:02:06 -05:00
|
|
|
files:
|
2021-03-24 12:08:59 -04:00
|
|
|
- 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 05:10:57 -05:00
|
|
|
md5sum: e2257263668dc8a75d95475099fb472d
|
2021-03-24 12:08:59 -04:00
|
|
|
- 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 05:10:57 -05:00
|
|
|
md5sum: 9eff7203596580cc5e42aceab4a469df
|
2021-07-21 04:00:48 -04:00
|
|
|
|
|
|
|
|
- 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
|
2021-07-23 05:44:00 -04:00
|
|
|
|
|
|
|
|
- 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
|