mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
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>
31 lines
1.4 KiB
YAML
31 lines
1.4 KiB
YAML
- name: salmon index
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command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
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tags:
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- salmon
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- salmon_index
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files:
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- path: ./output/salmon/salmon/ref_indexing.log
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- path: ./output/salmon/salmon/refseq.bin
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md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
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- path: ./output/salmon/salmon/versionInfo.json
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md5sum: 204865f645102587c4953fccb256797c
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- path: ./output/salmon/salmon/complete_ref_lens.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/mphf.bin
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md5sum: 53669a47610e33e031faafd32703b714
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- path: ./output/salmon/salmon/pre_indexing.log
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- path: ./output/salmon/salmon/ctable.bin
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- path: ./output/salmon/salmon/duplicate_clusters.tsv
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md5sum: 51b5292e3a874119c0e1aa566e95d70c
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- path: ./output/salmon/salmon/reflengths.bin
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md5sum: f57562f1fca3ae7b133f895ae13c3d08
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- path: ./output/salmon/salmon/info.json
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md5sum: 61ff4d3471134c280668355ddd39e99f
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- path: ./output/salmon/salmon/refAccumLengths.bin
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md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
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- path: ./output/salmon/salmon/ctg_offsets.bin
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md5sum: 27a76542337df436436e66017f66dd25
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- path: ./output/salmon/salmon/rank.bin
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md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
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- path: ./output/salmon/salmon/pos.bin
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- path: ./output/salmon/salmon/seq.bin
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