Merge pull request #174 from nf-core/PINTS-scatter-gather

PINTS scatter gather
nf-core · Nov 9, 2024 · 210b2fc · 210b2fc
2 parents 5bdce2e + 55861cd
commit 210b2fc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#142](https://github.com/nf-core/nascent/pull/142) - Updated CHM13 references
 - [#171](https://github.com/nf-core/nascent/pull/171) - Use assertAll in tests
 - [#165](https://github.com/nf-core/nascent/pull/165) - groHMM overhaul. Removed R mclapply calls and replaced with Nextflow scatter gather for parameter tuning. This creates a job for each parameter set.
+- [#174](https://github.com/nf-core/nascent/pull/174) - PINTS Scatter gather pattern by chromosome
 
 ### Fixed
 

diff --git a/conf/test_copro.config b/conf/test_copro.config
@@ -41,4 +41,7 @@ process {
             "-l 18"
         ].join(' ').trim()
     }
+    withName: 'NFCORE_NASCENT:NASCENT:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS:UMITOOLS_DEDUP' {
+        ext.args = "--unpaired-reads=discard --umi-separator=: --paired"
+    }
 }
diff --git a/docs/usage.md b/docs/usage.md
@@ -77,6 +77,14 @@ The current options for transcript identification include [GroHMM](https://bioco
 
 The default transcript identification option is PINTS, and HOMER if the transcript `assay_type` is `GROseq` but this may change in future releases.
 
+### PINTS
+
+PINTS handles the majority of the transcript identification, since it covers all of the supported assays.
+
+PINTS can use a lot of memory while running, so [a scatter-gather pattern was implemented](https://github.com/nf-core/nascent/blob/136a9ca2390121639e823e39e508afe9b6970d77/subworkflows/local/transcript_identification/main.nf#L47-L74).
+
+It splits the identification up by the chromosomes available in the provided FASTA file. Some of the chromosomes are skipped because PINTS throws an error when it doesn't find any regions. If this causes an issue with your analysis please open an issue.
+
 ### GroHMM
 
 groHMM is split into two steps: parameter tuning and transcript identification.

diff --git a/modules.json b/modules.json
@@ -150,7 +150,7 @@
                     },
                     "pints/caller": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "ac55541b663c35e9ff50f79d32049ce7492a6ea5",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/pints/caller/pints-caller.diff"
                     },
@@ -219,6 +219,11 @@
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
                     },
+                    "samtools/merge": {
+                        "branch": "master",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",

diff --git a/modules/nf-core/pints/caller/environment.yml b/modules/nf-core/pints/caller/environment.yml
diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf
diff --git a/modules/nf-core/pints/caller/meta.yml b/modules/nf-core/pints/caller/meta.yml
diff --git a/modules/nf-core/pints/caller/pints-caller.diff b/modules/nf-core/pints/caller/pints-caller.diff