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nf-core_modules/tests/software/salmon/quant/test.yml
Kevin Menden 4566525da2
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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- name: salmon quant single-end
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
tags:
- salmon
- salmon_quant
- salmon_quant_single_end
files:
- path: ./output/salmon/test/cmd_info.json
- path: ./output/salmon/test/quant.sf
md5sum: 687368b9963874c1797d210310b38516
- path: ./output/salmon/test/lib_format_counts.json
- path: ./output/salmon/test/quant.genes.sf
md5sum: ad4d31437f06db49b2436abeec29c78e
- path: ./output/salmon/test/logs/salmon_quant.log
- path: ./output/salmon/test/aux_info/expected_bias.gz
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/aux_info/meta_info.json
- path: ./output/salmon/test/aux_info/fld.gz
- path: ./output/salmon/test/aux_info/ambig_info.tsv
md5sum: 2ee3dc3080ad7222e0687481e7a1ee03
- path: ./output/salmon/test/aux_info/observed_bias.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: 2de170bdc9f6fd237d286429b292bb28
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/seq.bin
- name: salmon quant paired end
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
tags:
- salmon
- salmon_quant
- salmon_quant_paired_end
files:
- path: ./output/salmon/test/cmd_info.json
- path: ./output/salmon/test/quant.sf
md5sum: 4abd35d0a60b5279b394424f0e6ea42d
- path: ./output/salmon/test/lib_format_counts.json
- path: ./output/salmon/test/quant.genes.sf
md5sum: d750f8c9f248e30c3a6d0c2678bf9c6a
- path: ./output/salmon/test/logs/salmon_quant.log
- path: ./output/salmon/test/aux_info/expected_bias.gz
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
- path: ./output/salmon/test/aux_info/observed_bias_3p.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/aux_info/meta_info.json
- path: ./output/salmon/test/aux_info/fld.gz
- path: ./output/salmon/test/aux_info/ambig_info.tsv
md5sum: 33c0df069da554344869604ea8c18b22
- path: ./output/salmon/test/aux_info/observed_bias.gz
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: 221f754ed55dd1e34874f9b7b3f9d240
- path: ./output/salmon/salmon/ref_indexing.log
- path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- path: ./output/salmon/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/salmon/pre_indexing.log
- path: ./output/salmon/salmon/ctable.bin
- path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/pos.bin
- path: ./output/salmon/salmon/seq.bin
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