Merge pull request #427 from atrigila/add_pigz

Add nf-core `pigz uncompress`
nf-core · Sep 17, 2024 · 1e29e16 · 1e29e16
2 parents ef77e5c + a41a338
commit 1e29e16
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,7 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#405]](https://github.com/nf-core/smrnaseq/pull/405) - Fix [Umicollapse algo wrong set](https://github.com/nf-core/smrnaseq/issues/404) - Fix potential bug in Umicollapse (not effective as we do not allow PE data in smrnaseq - but for consistency)
 - [[#420]](https://github.com/nf-core/smrnaseq/pull/420) - Fix [mirTrace produces an error in test nextflex](https://github.com/nf-core/smrnaseq/issues/419) - Allow config mode to be used in mirtrace/qc
 - [[#425]](https://github.com/nf-core/smrnaseq/pull/425) - Raise [minimum required NXF version for pipeline](https://github.com/nf-core/smrnaseq/issues/424) - usage of `arity` in some modules now requires this
-- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/426) - replace local for nf-core `mirtop`
+- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/417) - replace local `mirtop`
+- [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
 - [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

diff --git a/conf/modules.config b/conf/modules.config
@@ -347,14 +347,7 @@ process {
             enabled: params.save_intermediates
         ]
     }
-    withName: 'MIRTOP_QUANT' {
-        publishDir = [
-            //mirtop already part of the output folder
-            path: { "${params.outdir}/mirna_quant/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
+
 
     // Mirtop
 
@@ -429,6 +422,12 @@ process {
     //
     // MIRDEEP
     //
+
+    withName: 'PIGZ_UNCOMPRESS' {
+        tag = {"${meta.id}"}
+        stageInMode = 'copy'
+    }
+
     withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER' {
         publishDir = [
             path: { "${params.outdir}/mirdeep2/mapper" },

diff --git a/conf/test_contamination_tech_reps.config b/conf/test_contamination_tech_reps.config
@@ -24,8 +24,7 @@ params {
     input      = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet_technical_repeats_short.csv'
 
     mirtrace_species         = 'hsa'
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
     skip_multiqc             = true
     skip_mirdeep             = true

diff --git a/conf/test_mirgenedb.config b/conf/test_mirgenedb.config
@@ -31,8 +31,7 @@ params {
     mirgenedb_species        = "Hsa"
 
     skip_mirdeep             = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
 }
 

diff --git a/conf/test_nextflex.config b/conf/test_nextflex.config
@@ -28,6 +28,7 @@ params {
     mirtrace_species    = 'hsa'
 
     skip_mirdeep             = true
+    save_intermediates       = true
 
 }
 

diff --git a/conf/test_skipfastp.config b/conf/test_skipfastp.config
@@ -29,8 +29,7 @@ params {
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
     skip_fastp               = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 }
 
 // Do not include any additional config so it defaults to protocol custom
diff --git a/conf/test_technical_repeats.config b/conf/test_technical_repeats.config
@@ -26,8 +26,7 @@ params {
 
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
-    save_merged              = false
-    save_aligned_mirna_quant = false
+    save_intermediates       = true
 
     skip_fastqc                 = true
     skip_multiqc                = true

diff --git a/conf/test_umi.config b/conf/test_umi.config
@@ -30,9 +30,10 @@ params {
 
     //UMI Specific testcase
     with_umi = true
-    umitools_extract_method = 'regex'
-    umitools_bc_pattern = '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)'
-    save_umi_intermeds = true
+    umitools_extract_method  = 'regex'
+    umitools_bc_pattern      = '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)'
+    save_umi_intermeds       = true
+    save_intermediates       = true
 }
 
 // Include illumina config to run test without additional profiles

diff --git a/modules.json b/modules.json
@@ -65,6 +65,11 @@
                         "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
+                    "pigz/uncompress": {
+                        "branch": "master",
+                        "git_sha": "c00055a0b13d622b4f1f51a8e5be31deaf99ded7",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",

diff --git a/modules/local/mirdeep2_prepare.nf b/modules/local/mirdeep2_prepare.nf
diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
diff --git a/modules/nf-core/pigz/uncompress/main.nf b/modules/nf-core/pigz/uncompress/main.nf
diff --git a/modules/nf-core/pigz/uncompress/meta.yml b/modules/nf-core/pigz/uncompress/meta.yml
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test b/modules/nf-core/pigz/uncompress/tests/main.nf.test
diff --git a/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap b/modules/nf-core/pigz/uncompress/tests/main.nf.test.snap
diff --git a/modules/nf-core/pigz/uncompress/tests/tags.yml b/modules/nf-core/pigz/uncompress/tests/tags.yml
diff --git a/subworkflows/local/mirdeep2.nf b/subworkflows/local/mirdeep2.nf
@@ -2,7 +2,7 @@
 // Quantify mirna with bowtie and mirtop
 //
 
-include { MIRDEEP2_PIGZ   } from '../../modules/local/mirdeep2_prepare'
+include { PIGZ_UNCOMPRESS } from '../../modules/nf-core/pigz/uncompress/main'
 include { MIRDEEP2_MAPPER } from '../../modules/local/mirdeep2_mapper'
 include { MIRDEEP2_RUN    } from '../../modules/local/mirdeep2_run'
 
@@ -17,10 +17,10 @@ workflow MIRDEEP2 {
     main:
     ch_versions = Channel.empty()
 
-    MIRDEEP2_PIGZ ( reads )
-    ch_versions = ch_versions.mix(MIRDEEP2_PIGZ.out.versions.first())
+    PIGZ_UNCOMPRESS ( reads )
+    ch_versions = ch_versions.mix(PIGZ_UNCOMPRESS.out.versions.first())
 
-    MIRDEEP2_MAPPER ( MIRDEEP2_PIGZ.out.reads, index )
+    MIRDEEP2_MAPPER ( PIGZ_UNCOMPRESS.out.file, index )
     ch_versions = ch_versions.mix(MIRDEEP2_MAPPER.out.versions.first())
 
     MIRDEEP2_RUN ( fasta.map{meta,file->file}, MIRDEEP2_MAPPER.out.mirdeep2_inputs, hairpin, mature )

diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf
@@ -19,7 +19,6 @@ include {   BAM_SORT_STATS_SAMTOOLS as BAM_STATS_MATURE
             BAM_SORT_STATS_SAMTOOLS as BAM_STATS_HAIRPIN   } from '../nf-core/bam_sort_stats_samtools'
 
 include { SEQCLUSTER_COLLAPSE  } from '../../modules/nf-core/seqcluster/collapse/main'
-include { MIRTOP_QUANT         } from '../../modules/local/mirtop_quant.nf'
 include { TABLE_MERGE          } from '../../modules/local/datatable_merge/datatable_merge.nf'
 include { EDGER_QC             } from '../../modules/local/edger_qc/edger_qc.nf'
 include { BAM_STATS_MIRNA_MIRTOP } from '../../subworkflows/nf-core/bam_stats_mirna_mirtop/main'
-Original file line number
+Diff line change
@@ Expand Up / @@ -28,6 +28,7 @@ params { @@
         mirtrace_species    = 'hsa'
         skip_mirdeep             = true
+        save_intermediates       = true
     }
@@ Expand Down @@