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nf-core_modules/tests/software/quast/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: quast with reference
command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
tags:
- quast
- quast_reference
files:
- path: ./output/quast/report.tsv
- path: ./output/quast/quast/transposed_report.txt
md5sum: 73ae4f7cbe0da640819214cb013a79ef
- path: ./output/quast/quast/transposed_report.tex
md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449
- path: ./output/quast/quast/icarus.html
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 475bf9987c421b72fe1675b54ae0bcbe
- path: ./output/quast/quast/report.tex
md5sum: e4c1d12bfe94d5a10e2264397bb90f83
- path: ./output/quast/quast/report.txt
md5sum: 6295e6d462b1db45b1bb9f3f508275ad
- path: ./output/quast/quast/report.tsv
md5sum: b70404d2b4d4e905afcfe3d149a5bd15
- path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/genome_stats/test_transcriptome_genomic_features_any.txt
md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
- path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
- path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
- path: ./output/quast/quast/genome_stats/genome_info.txt
md5sum: a4bb1f2792c175fc8d7fbf37f219e552
- path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt
md5sum: c52381f09ea40b6141be5232494727b6
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_transcriptome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/gc.icarus.txt
md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
- path: ./output/quast/quast/basic_stats/NGx_plot.pdf
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
- path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.mis_contigs.info
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.unaligned.info
md5sum: a8505cf206bf53ca369f7e3073fee587
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
md5sum: 4895cb02a010f1db85fc4992ac3c63b1
- path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
md5sum: d5c9dd22ce8f382649f74ba1f61d8a84
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout
- path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv
md5sum: c247152eb82b361106492642fd796e2c
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
md5sum: 0df52940978f10c0fc9ed5f6770f170e
- path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
md5sum: d83abdf60e7ef02354a783dff4262d7d
- path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
md5sum: f2adf811a611abdcb9f10bd7801e61e1
- path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
md5sum: dd6e08408ea9a6830d47d5c21b84d587
- path: ./output/quast/quast/contigs_reports/unaligned_report.txt
- path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
md5sum: e77d87bafe0e2c881805f8dfcc5f2351
- path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr
- path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
- path: ./output/quast/quast/contigs_reports/unaligned_report.tex
md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered
md5sum: ec9191d0acb5d5bce56b4842551a8598
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords
md5sum: dda3fc0addc41ecc0d5183dee6f95886
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.used_snps.gz
md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords_tmp
md5sum: ce66eaeb99fdc11e4d50efadc1816e04
- path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
- name: quast without reference
command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
tags:
- quast
- quast_no_reference
files:
- path: ./output/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
- path: ./output/quast/quast/transposed_report.txt
md5sum: 5496230d4bc3846616d7e08d52ffc081
- path: ./output/quast/quast/transposed_report.tex
md5sum: cf6a3b50575b510a7c42f5e745dd8674
- path: ./output/quast/quast/icarus.html
md5sum: ba0ddcdbcd743191d282e3986cb68735
- path: ./output/quast/quast/transposed_report.tsv
md5sum: 4b128bbf595b07dd2e2d5230bf575d29
- path: ./output/quast/quast/report.tex
md5sum: ac22b93fad7cdb6a812e5f670e815647
- path: ./output/quast/quast/report.txt
md5sum: 283160faa1d8cd32064c49e3c6d738d5
- path: ./output/quast/quast/report.tsv
md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
- path: ./output/quast/quast/report.html
- path: ./output/quast/quast/report.pdf
- path: ./output/quast/quast/quast.log
- path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
- path: ./output/quast/quast/basic_stats/Nx_plot.pdf
- path: ./output/quast/quast/basic_stats/test_genome_GC_content_plot.pdf
- path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
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