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nf-core_modules/tests/modules
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Edmund Miller c19671dca9
Subworkflow Infrastructure (#662) 
* feat(subworkflows): Add align_bowtie2 subworkflow

For testing CI setup

* test(align_bowtie2): Add initial list of changes to test

* test(align_bowtie2): Add initial test

* refactor: Use tags to run subworkflows ci

For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.

* refactor: Use individual directories for subworkflows

* docs(align_bowtie2): Add initial meta.yml

Copied most of it from the bowtie2/align module.

* fix(align_bowtie2): Fix module include paths

* test(bam_sort_samtools): Add initial test

* ci(bam_sort_samtools): Add modules that trigger the tag

* test(bam_stats_samtools): Add initial test

* ci(bam_stats_samtools): Add keys to pick up changes

* docs(bam_samtools): Add initial meta.yml

* test(align_bowtie2): Fix path to subworkflow

* test(align_bowtie2): Update entry point

* fix(bam_sort_samtools): Update include paths

* test(bam_sort_samtools): Fix path

* style: Clean up addParams

* test(samtools_sort): Add suffix for test

* test(align_bowtie2): Add samtools_options for suffix

* test(bam_stats_samtools): Update path

* test(bam_stats_samtools): Use stats input

Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow

* ci(linting): Skip module linting of subworkflows

* ci(linting): Clean up startsWith statement

* test(bam_stats_samtools): Use single end test data for single end test

* test(bam_stats_samtools): Add expected files

* test(align_bowtie2): Add paired-end test

* test(align_bowtie2): Sort order of output

* test(align_bowtie2): Update hashes

* docs(align_bowtie2): Fix typo

* test(align_bowtie2): Update samtools output names

* test(align_bowtie2): Remove md5sums for bam/bai

* feat(subworkflows): Add nextflow.configs

These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.

* docs(subworkflows): Include modules instead of tools

* fix: Update to versions

* chore(align_bowtie2): Remove duplicate tag

* style: Format yamls

* test(subworkflows): Only check versions for modules

* chore: Update subworkflows to match rnaseq dev

* fix(subworkflows): Update paths

* fix(bam_sort_samtools): Fix sort parameters for testing

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* docs: Update TODOs with a message

* ci: Try using a matrix for strategy

* ci: Try passing an array

* Revert "ci: Try passing an array"

This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-08 16:02:42 +01:00
..
abacas Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
adapterremoval Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
agrvate module for agrvate (#693) 2021-09-16 12:42:23 +02:00
allelecounter Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
amps add Amps (#768) 2021-09-30 12:54:16 +02:00
arriba Added module arriba (#611) 2021-07-22 15:19:42 +01:00
artic Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bamaligncleaner Add module: bamaligncleaner (#676) 2021-09-15 10:31:49 +02:00
bandage/image Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bbmap Add bbmap/bbsplit module (#771) 2021-09-30 13:37:35 +01:00
bcftools Add bcftools/query module (#670) 2021-09-14 09:19:01 +02:00
bedtools Add bedtools/makewindows module (#658) 2021-09-07 14:36:06 -04:00
bismark Fix version commands (#749) 2021-09-27 22:10:37 +01:00
blast nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bowtie Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bowtie2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwa Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
bwamem2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwameth Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
cat Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
chromap Chromap Module (#659) 2021-09-15 17:20:55 +01:00
cnvkit Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cooler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
csvtk/concat add csvtk/concat module (#785) 2021-10-05 21:48:47 +01:00
custom/dumpsoftwareversions Correct parsing versions with trailing zeros (#795) 2021-10-06 08:16:36 +02:00
cutadapt Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
damageprofiler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
deeptools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
delly/call few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
diamond Diamond (#710) 2021-09-23 09:13:04 +01:00
dragonflye add module for dragonflye (#633) 2021-08-16 11:51:30 +02:00
dshbio Add dsh-bio export-segments module (#631) 2021-08-17 15:53:41 +02:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
expansionhunter Expansionhunter (#666) 2021-08-16 17:47:42 +02:00
fastani module fastani (#695) 2021-09-21 20:20:26 +01:00
fastp enhance module fastp: add save_merged (#598) (#614) 2021-07-23 10:44:00 +01:00
fastqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fasttree Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fgbio Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
flash Fix flash and cat/fastq modules (#759) 2021-09-28 21:14:11 +01:00
gatk4 Learnreadorientationmodel (#794) 2021-10-07 13:55:06 +01:00
genmap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
gffread Fix bug in gffread (#686) 2021-09-15 19:55:08 +01:00
glnexus Add glnexus (#729) 2021-09-22 13:31:01 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gtdbtk/classifywf Add gtdbtk/classifywf module (#765) 2021-10-05 21:23:01 +01:00
gubbins nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
gunzip Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
hicap add hicap module (#772) 2021-10-05 21:42:09 +01:00
hifiasm few version and test data config fixes (#758) 2021-09-28 20:42:04 +01:00
hisat2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
hmmer/hmmalign Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
homer Homer Modules (#75) 2021-09-08 15:40:34 +00:00
iqtree Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
ismapper add ismapper module (#773) 2021-10-05 21:55:41 +01:00
isoseq3 New module: isoseq3/cluster (#801) 2021-10-07 10:06:02 +01:00
ivar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
kallisto/index Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kallistobustools Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
kleborate Add module kleborate (#711) 2021-09-21 20:45:42 +01:00
kraken2/kraken2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
last nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
lima New module: LIMA (#719) 2021-09-27 16:14:35 +01:00
lofreq fix: lofreq/callparallel missing arg (#562) (#586) 2021-07-19 09:19:27 +01:00
malt update: MALT build version bump (#699) 2021-09-15 16:46:29 +01:00
maltextract add: MALTEXTRACT (#725) 2021-09-21 19:57:27 +01:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
mashtree add mashtree module (#767) 2021-10-05 21:27:30 +01:00
metaphlan3 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
methyldackel Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minia Fix version commands (#749) 2021-09-27 22:10:37 +01:00
minimap2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
mlst added classic mlst module (#742) 2021-10-05 20:49:46 +01:00
mosdepth Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
multiqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
muscle Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanolyse Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanoplot Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nextclade Update Nextclade to output all files by default (#638) 2021-07-28 19:49:50 +01:00
optitype Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairix Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pangolin Update pangolin to 3.1.11 (#721) 2021-09-20 19:59:05 +01:00
pbbam/pbmerge New module: pbbam/pbmerge (#752) 2021-10-05 23:16:45 +01:00
pbccs new module: pbccs (#688) 2021-09-16 11:48:18 +01:00
picard Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
pirate add pirate module (#777) 2021-10-05 22:28:25 +01:00
plasmidid Fix yml ver (#756) 2021-09-28 18:33:07 +02:00
plink/vcf Adding plink/vcf module (#656) 2021-09-14 08:51:40 +02:00
preseq/lcextrap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prodigal Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prokka Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pycoqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pydamage Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
qcat Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qualimap/bamqc Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
quast Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rapidnj Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rasusa Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
raxmlng Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
roary add roary module (#776) 2021-10-05 22:08:47 +01:00
rsem Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
rseqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
salmon Fix version commands (#749) 2021-09-27 22:10:37 +01:00
samtools Subworkflow Infrastructure (#662) 2021-10-08 16:02:42 +01:00
seacr/callpeak Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqkit/split2 Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqtk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sequenzautils Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
seqwish/induce Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
shovill Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpdists module: snp-dists (#697) 2021-09-15 16:36:49 +01:00
snpeff Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpsites Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
spades nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
spatyper add spatyper module (#784) 2021-10-05 22:21:35 +01:00
staphopiasccmec add staphopia-sccmec module (#702) 2021-09-15 17:24:11 +01:00
star Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
strelka/germline Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
stringtie Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
subread/featurecounts fix more ver yml (#757) 2021-09-28 20:25:10 +01:00
tabix nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
tiddit/sv Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
trimgalore Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
ucsc Fix version commands: round 3 (#754) 2021-09-28 14:37:47 +01:00
unicycler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
untar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
unzip Unzip update (#730) 2021-09-22 11:02:32 +01:00
variantbam Add variantbam (#618) 2021-07-26 19:07:29 +01:00
vcftools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
yara fix more ver yml (#757) 2021-09-28 20:25:10 +01:00