Merge remote-tracking branch 'upstream/dev' into dev_remove_getscale

nf-core · Jul 14, 2023 · fc4b412 · fc4b412
2 parents b624cee + 1bef3c1
commit fc4b412
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Showing 7 changed files with 5 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,9 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.0.0 - [07/10/2023]
+## v2.0.0 - [07/13/2023]
 
-- update to [nf-core-template-2.9](https://github.com/nf-core/hicar/pull/89#issue-1797065776)
+- [[#89](https://github.com/nf-core/hicar/pull/89)] - update to nf-core-template-2.9
+- [[#90](https://github.com/nf-core/hicar/pull/90)] - remove the output folder setting from config files
 - [replace the dots](https://github.com/nf-core/hicar/pull/89#issue-1797065776) by '\_' in the samples group
 - add [support for MseI](https://github.com/jianhong/hicar/commit/64bfcecab9870100d56631ffc31ff0ed471e1255).
 - add TAD, AB compartments, APA analysis (see available tools in usage documentation)

diff --git a/conf/test.config b/conf/test.config
@@ -22,9 +22,6 @@ params {
     // Input data
     input = "${projectDir}/assets/test_multi_samplesheet.csv"
 
-    // Output folder
-    outdir = 'results'
-
     // peak calculating
     maps_cutoff_counts = 6
     maps_cutoff_fold_change = 2

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,9 +17,6 @@ params {
     // Input data for full size test
     input = "${projectDir}/assets/test_full_samplesheet.csv"
 
-    // Output folder
-    outdir = 'results'
-
     // peak calculating
     maps_cutoff_counts = 6
     maps_cutoff_fold_change = 2

diff --git a/conf/test_hichip.config b/conf/test_hichip.config
@@ -24,9 +24,6 @@ params {
     method = 'HiChIP'
     anchor_peaks = 'https://raw.githubusercontent.com/aryeelab/hichipper/master/tests/chipseq/GM12878_SMC3_ChIPSeq_chr22.narrowPeak'
 
-    // Output folder
-    outdir = 'results'
-
     // peak calculating
     maps_cutoff_counts = 6
     maps_cutoff_fold_change = 2

diff --git a/conf/test_hipeak.config b/conf/test_hipeak.config
@@ -20,9 +20,6 @@ params {
     // Input data for full size test
     input = "${projectDir}/assets/test_multi_samplesheet.csv"
 
-    // Output folder
-    outdir = 'results'
-
     // peak calculating
     maps_cutoff_counts = 6
     maps_cutoff_fold_change = 2

diff --git a/conf/test_multi.config b/conf/test_multi.config
@@ -20,9 +20,6 @@ params {
     // Input data for full size test
     input = "${projectDir}/assets/test_multi_samplesheet.csv"
 
-    // Output folder
-    outdir = 'results'
-
     // peak calculating
     maps_cutoff_counts = 6
     maps_cutoff_fold_change = 2

diff --git a/workflows/hicar.nf b/workflows/hicar.nf
@@ -180,8 +180,8 @@ workflow HICAR {
     ch_reads = Channel.fromSamplesheet("input")
         .map{
             meta, fastq_1, fastq_2 ->
-                meta = meta - meta.subMap(['id', 'single_end', 'group']) + [id: meta.group.toString().replaceAll("\\.", "_") + "_REP" + meta.replicate + "_T" + meta.techniquereplicate, single_end: false, group: meta.group.toString().replaceAll("\\.", "_")]
-                [meta, [fastq_1, fastq_2]]
+                meta_copy = meta - meta.subMap(['id', 'single_end', 'group']) + [id: meta.group.toString().replaceAll("\\.", "_") + "_REP" + meta.replicate + "_T" + meta.techniquereplicate, single_end: false, group: meta.group.toString().replaceAll("\\.", "_")]
+                [meta_copy, [fastq_1, fastq_2]]
         }
     //
     // check the input fastq files are correct