Reduce spec of PR

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`
 

conf/test.config

@@ -12,8 +12,8 @@
 
 process {
     resourceLimits = [
-        cpus: 2,
-        memory: '2.GB',
+        cpus: 4,
+        memory: '15.GB',
         time: '1.h'
     ]
 }

conf/test_all.config

@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 2,
-        memory: '7.GB',
+        memory: '10.GB',
         time: '1.h'
     ]
 }

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"

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))