diff --git a/CHANGELOG.md b/CHANGELOG.md index 69c25dbf..afa92adc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,7 +64,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co - [#148](https://github.com/nf-core/phaseimpute/pull/148) - Fix awsfulltest github action for manual dispatch - [#149](https://github.com/nf-core/phaseimpute/pull/149) - Remove the map file from the awsfulltest - [#152](https://github.com/nf-core/phaseimpute/pull/152) - Fix URLs in the documentation and remove tools citation in the README, use a white background for all images in the documentation. -- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Remove normalisation, frequency commputation and phasing from full test to reduce cost and computational time. Simplify subworkflows snapshot and check only for files names (no md5sum for bam and vcf files). +- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Update and simplify subworkflows snapshot and check only for files names (no md5sum for bam and vcf files due to timestamp). ### `Fixed` @@ -74,7 +74,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co - [#75](https://github.com/nf-core/phaseimpute/pull/75) - Set frequency computation with VCFFIXUP process as optional with `--compute_freq`. Use Glimpse_chunk on panel vcf to compute the chunk and not makewindows on fasta. - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV. - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`. -- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necesary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input. +- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necesary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input. ### `Dependencies` diff --git a/conf/test.config b/conf/test.config index 8a7c8c2b..f5c7b8dd 100644 --- a/conf/test.config +++ b/conf/test.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '15.GB', time: '1.h' ] } diff --git a/conf/test_all.config b/conf/test_all.config index c1b0057f..854f8664 100644 --- a/conf/test_all.config +++ b/conf/test_all.config @@ -13,7 +13,7 @@ process { resourceLimits = [ cpus: 2, - memory: '7.GB', + memory: '10.GB', time: '1.h' ] } diff --git a/conf/test_full.config b/conf/test_full.config index f4048ae4..fa1e3475 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -36,8 +36,8 @@ params { // Panelprep optional args remove_samples = "NA12878,NA12891,NA12892" normalize = true - compute_freq = false - phase = false + compute_freq = true + phase = true // Impute tools tools = "glimpse1" diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf index 52215c6a..f48d3631 100644 --- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf @@ -275,25 +275,6 @@ workflow PIPELINE_INITIALISATION { .collect() .subscribe { log.info "The following contigs will be processed: ${it}" } - // Remove other contigs from panel and posfile files - ch_panel = ch_panel - .combine(ch_regions.collect{ it[0]["chr"]}.toList()) - .filter { meta, _vcf, _index, chrs -> - meta.chr in chrs - } - .map {meta, vcf, index, _chrs -> - [meta, vcf, index] - } - - ch_posfile = ch_posfile - .combine(ch_regions.collect{ it[0]["chr"]}.toList()) - .filter { meta, _vcf, _index, _hap, _legend, chrs -> - meta.chr in chrs - } - .map {meta, vcf, index, hap, legend, _chrs -> - [meta, vcf, index, hap, legend] - } - // Check that all input files have the correct index checkFileIndex(ch_input.mix(ch_input_truth, ch_ref_gen, ch_panel))