Svyatoslav Sidorov
95dfa7bc8d
Enhance bedtools ( #557 )
...
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Generalized intersect and genomecov
* Finished subtract and tests for intersect and genomecov
* Finished up meta YAMLs
* Replaced functions.nf in subtract
* do not add "." in prefix when suffix is set (#550 )
when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc.
I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules.
##' Ref:
https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900
* Modules TLC (#551 )
* Modules TLC
* Fix all the tests
* Fix linting failures (#552 )
* Modules TLC
* Fix all the tests
* Fix linting failures
* Soft-link build files to bypass lint error
* Update software/rseqc/junctionannotation/main.nf
* Fix rsem (#555 )
* bump bcftools filter
* fix bcftools
* rsem/preparereference
* added calculateexpression
* meta.yml and pytest_software
* paired end
* add test.yml
* fix rseqc/junctionsaturation (#553 )
* bump bcftools filter
* junctionsaturation meta.yml and test
* pytest config entry
* bump bcftools version down again
* fix test
* fix bcftools
* Adapt linting action (#556 )
* bump bcftools filter
* fix bcftools
* adapt module linting
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixed variable names in intersect and genomecov
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: riederd <dietmar.rieder@i-med.ac.at>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-07-07 09:44:09 +01:00
Harshil Patel
466ab67808
Fixes for nanoseq modules ( #479 )
...
* Fix minimap2 index module
* Fix minimap2 index tests
* Fix graphmap2 index module
* Fix graphmap2 module
* Fix ECLint
* Fix bedtools bamtobed module
* Fix tests for bedtools bamtobed module
* Add tag for graphmap2 align module
* Fix EClint
* Fix qcat module
* Add md5sum for graphmap2/align module
* Remove non-started test data file
* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00
Yuk Kei Wan
3f804ee667
add bedtools bamtobed module (from nanoseq modules) ( #466 )
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* add bedtools bamtobed module
* fix erros
* fix linting problem
2021-04-30 13:20:31 +01:00
Edmund Miller
a3684d9594
Lint modules ci ( #389 )
...
* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
Harshil Patel
c7155d023e
Update bedtools modules with config logic ( #369 )
2021-03-24 14:14:19 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
...
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +00:00
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
Harshil Patel
28866f3dc7
Update tests/software/bedtools/maskfasta/main.nf
2021-02-09 21:36:38 +00:00
Harshil Patel
aaa088dba8
Update tests/software/bedtools/getfasta/main.nf
2021-02-09 21:34:29 +00:00
JoseEspinosa
e118bc049a
Add bedtools getfasta module
2021-02-09 17:56:51 +01:00
JoseEspinosa
7536b386a5
Correct channel declaration on bedtools_maskfasta
2021-02-09 17:56:01 +01:00
Harshil Patel
46e5df2cf7
Merge pull request #151 from drpatelh/bedtools
...
Follow up fixes for bedtools modules added in #79
2021-02-09 01:54:31 +00:00
JoseEspinosa
1b3e5e0283
Fixing module name in test.yml
2021-02-08 23:45:01 +01:00
JoseEspinosa
02d10c25a3
Add bedtools maskfasta module
2021-02-08 23:41:10 +01:00
drpatelh
0b9e32e32d
Remove complement suffix from tests
2021-02-08 22:25:13 +00:00
drpatelh
5779b180da
Fix bedtools sort module
2021-02-07 21:32:43 +00:00
drpatelh
f3b5af4ed5
Fix bedtools slip module
2021-02-07 21:32:20 +00:00
drpatelh
38964ecfc0
Fix bedtools intersect module
2021-02-07 21:32:01 +00:00
drpatelh
a37b116186
Fix bedtools merge module
2021-02-07 21:31:39 +00:00
drpatelh
4564ef0e54
Fix bedtools genomecov module
2021-02-07 21:31:21 +00:00
drpatelh
a0c08e0c06
Fix bedtools complement module
2021-02-07 21:31:02 +00:00
Harshil Patel
0393d39105
Update tests/software/bedtools/complement/main.nf
2021-02-07 20:35:51 +00:00
Harshil Patel
5269c1ec60
Update tests/software/bedtools/intersect/main.nf
2021-02-07 20:35:12 +00:00
Harshil Patel
8841af1267
Update tests/software/bedtools/merge/main.nf
2021-02-07 20:34:30 +00:00
Harshil Patel
b068f2fc53
Update tests/software/bedtools/sort/main.nf
2021-02-07 20:33:02 +00:00
sruthipsuresh
7a1c2a2eb5
Fixed slop module
2021-01-29 23:17:44 -06:00
sruthipsuresh
93e414635b
Fixed md5sum, fixed filters, fixed slop input
2021-01-29 23:17:44 -06:00
sruthipsuresh
78ac4435be
Added new tests, todo: fix md5sums
2021-01-29 23:17:44 -06:00
Edmund Miller
2b0d51ca9c
test(bedtools): Remove old style tests
...
AKA how the tests were done last week.
2021-01-29 23:17:44 -06:00
Edmund Miller
7d52907d1c
test(bedtools): Fix typo on yaml indentation
2021-01-29 23:17:44 -06:00
sruthipsuresh
ac7f634675
Added complement test
2021-01-29 23:17:44 -06:00
sruthipsuresh
e360617ac6
Fixed images, genomecov
2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc
Fixed slop file
2021-01-29 23:17:44 -06:00
sruthipsuresh
29639c522f
Corrected sort
2021-01-29 23:17:44 -06:00
sruthipsuresh
a108bd407e
Corrected md5sum and output
2021-01-29 23:17:44 -06:00
sruthipsuresh
2f19b4279c
All modules corrected, TODO config
2021-01-29 23:17:44 -06:00
sruthipsuresh
32564137fd
Corrected workflows and ran editor config
2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af
rebased and updated all bedtools testing and modules
2021-01-29 23:17:44 -06:00
