2021-02-03 16:02:58 +00:00
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- name: bowtie2 align single-end
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2021-02-03 16:44:56 +00:00
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command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
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2021-02-03 16:02:58 +00:00
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tags:
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- bowtie2
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2021-04-08 08:10:52 +00:00
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- bowtie2/align
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2021-02-03 16:02:58 +00:00
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files:
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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
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- path: ./output/bowtie2/test.bam
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- path: ./output/bowtie2/test.bowtie2.log
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.3.bt2
|
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
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md5sum: 4ed93abba181d8dfab2e303e33114777
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.2.bt2
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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
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md5sum: 47b153cd1319abc88dda532462651fcf
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.1.bt2
|
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
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md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.4.bt2
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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
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md5sum: c25be5f8b0378abf7a58c8a880b87626
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.rev.1.bt2
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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
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md5sum: 52be6950579598a990570fbcf5372184
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2021-03-24 18:29:41 +00:00
|
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- path: ./output/index/bowtie2/genome.rev.2.bt2
|
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
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md5sum: e3b4ef343dea4dd571642010a7d09597
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2021-02-03 16:02:58 +00:00
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- name: bowtie2 align paired-end
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2021-02-03 16:44:56 +00:00
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command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
|
2021-02-03 16:02:58 +00:00
|
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|
tags:
|
|
|
|
|
- bowtie2
|
2021-04-08 08:10:52 +00:00
|
|
|
- bowtie2/align
|
2021-02-03 16:02:58 +00:00
|
|
|
files:
|
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
|
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- path: ./output/bowtie2/test.bam
|
|
|
|
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- path: ./output/bowtie2/test.bowtie2.log
|
2021-03-24 18:29:41 +00:00
|
|
|
- path: ./output/index/bowtie2/genome.3.bt2
|
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
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md5sum: 4ed93abba181d8dfab2e303e33114777
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.2.bt2
|
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
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md5sum: 47b153cd1319abc88dda532462651fcf
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2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.1.bt2
|
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
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md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
|
2021-03-24 18:29:41 +00:00
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- path: ./output/index/bowtie2/genome.4.bt2
|
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
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md5sum: c25be5f8b0378abf7a58c8a880b87626
|
2021-03-24 18:29:41 +00:00
|
|
|
- path: ./output/index/bowtie2/genome.rev.1.bt2
|
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
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md5sum: 52be6950579598a990570fbcf5372184
|
2021-03-24 18:29:41 +00:00
|
|
|
- path: ./output/index/bowtie2/genome.rev.2.bt2
|
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
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md5sum: e3b4ef343dea4dd571642010a7d09597
|