Merge pull request #382 from JoseEspinosa/fixes

Set chromap to no shift reads by default
nf-core · Oct 11, 2024 · ed7a5cf · ed7a5cf
2 parents ea927b5 + e060f4a
commit ed7a5cf
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Showing 11 changed files with 246 additions and 39 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,7 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#359](https://github.com/nf-core/atacseq/issues/359)] - Fix `--save_unaligned` description in schema.
 - [[#344](https://github.com/nf-core/atacseq/issues/344)] - Fix memory issues when sorting merged replicates after `bedtools genomecov`.
 - [[#338](https://github.com/nf-core/atacseq/issues/338)] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores.
-- [[#370](https://github.com/nf-core/atacseq/issues/370)] - Adding line numbers to errors messages in `bin/check_samplesheet.py`
+- [[#370](https://github.com/nf-core/atacseq/issues/370)] - Adding line numbers to errors messages in `bin/check_samplesheet.py`.
+- [[#381](https://github.com/nf-core/atacseq/issues/381)] - Set chromap to no shift reads by default and install `deeptools/alignmentsieve` from modules.
 
 ### Parameters
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -286,7 +286,12 @@ if (params.aligner == 'chromap') {
         }
 
         withName: 'CHROMAP_CHROMAP' {
-            ext.args   = '-l 2000 --Tn5-shift --low-mem --SAM'
+            ext.args   = [
+                '-l 2000',
+                '--low-mem',
+                '--SAM',
+                params.shift_reads ? '--Tn5-shift' : ''
+            ].join(' ').trim()
             ext.prefix = { "${meta.id}.Lb" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/library" },

diff --git a/modules.json b/modules.json
@@ -50,6 +50,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "deeptools/alignmentsieve": {
+                        "branch": "master",
+                        "git_sha": "5c2ab5de7e8de33ac7cab83a4cd28a4d29a84049",
+                        "installed_by": ["modules"]
+                    },
                     "deeptools/computematrix": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/local/deeptools_alignmentsieve.nf b/modules/local/deeptools_alignmentsieve.nf
diff --git a/modules/nf-core/deeptools/alignmentsieve/environment.yml b/modules/nf-core/deeptools/alignmentsieve/environment.yml
diff --git a/modules/nf-core/deeptools/alignmentsieve/main.nf b/modules/nf-core/deeptools/alignmentsieve/main.nf
diff --git a/modules/nf-core/deeptools/alignmentsieve/meta.yml b/modules/nf-core/deeptools/alignmentsieve/meta.yml
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml b/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml
diff --git a/subworkflows/local/bam_shift_reads.nf b/subworkflows/local/bam_shift_reads.nf
@@ -1,7 +1,7 @@
 include { SAMTOOLS_SORT            } from '../../modules/nf-core/samtools/sort/main'
 include { SAMTOOLS_INDEX           } from '../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_FLAGSTAT        } from '../../modules/nf-core/samtools/flagstat/main'
-include { DEEPTOOLS_ALIGNMENTSIEVE } from '../../modules/local/deeptools_alignmentsieve'
+include { DEEPTOOLS_ALIGNMENTSIEVE } from '../../modules/nf-core/deeptools/alignmentsieve'
 
 workflow BAM_SHIFT_READS {
     take: