mirror of
https://github.com/MillironX/nf-core_modules.git
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4566525da2
* 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>
43 lines
2.1 KiB
YAML
43 lines
2.1 KiB
YAML
- name: stringtie forward-strand
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command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
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tags:
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- stringtie
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files:
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- path: ./output/test_stringtie_forward/test.transcripts.gtf
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md5sum: cbce87f06598eb756e7670ba3217a42f
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- path: ./output/test_stringtie_forward/test.gene.abundance.txt
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md5sum: 7d8bce7f2a922e367cedccae7267c22e
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- path: ./output/test_stringtie_forward/test.coverage.gtf
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: ./output/test_stringtie_forward/test.ballgown/e_data.ctab
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md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
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- path: ./output/test_stringtie_forward/test.ballgown/i_data.ctab
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md5sum: be3abe09740603213f83d50dcf81427f
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- path: ./output/test_stringtie_forward/test.ballgown/t_data.ctab
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md5sum: 3b66c065da73ae0dd41cc332eff6a818
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- path: ./output/test_stringtie_forward/test.ballgown/i2t.ctab
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md5sum: 8a117c8aa4334b4c2d4711932b006fb4
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- path: ./output/test_stringtie_forward/test.ballgown/e2t.ctab
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md5sum: e981c0038295ae54b63cedb1083f1540
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- name: stringtie reverse-strand
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command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
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tags:
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- stringtie
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files:
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- path: ./output/test_stringtie_reverse/test.transcripts.gtf
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md5sum: bb992085e42bad19877c847dae496c80
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- path: ./output/test_stringtie_reverse/test.gene.abundance.txt
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md5sum: 7385b870b955dae2c2ab78a70cf05cce
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- path: ./output/test_stringtie_reverse/test.coverage.gtf
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: ./output/test_stringtie_reverse/test.ballgown/e_data.ctab
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md5sum: 879b6696029d19c4737b562e9d149218
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- path: ./output/test_stringtie_reverse/test.ballgown/i_data.ctab
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md5sum: be3abe09740603213f83d50dcf81427f
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- path: ./output/test_stringtie_reverse/test.ballgown/t_data.ctab
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md5sum: 3b66c065da73ae0dd41cc332eff6a818
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- path: ./output/test_stringtie_reverse/test.ballgown/i2t.ctab
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md5sum: 8a117c8aa4334b4c2d4711932b006fb4
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- path: ./output/test_stringtie_reverse/test.ballgown/e2t.ctab
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md5sum: e981c0038295ae54b63cedb1083f1540
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