Merge pull request #438 from atrigila/update_mirtop

nf-core · Sep 20, 2024 · 46865dd · 46865dd
2 parents 774742f + db1cf98
commit 46865dd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#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`.
 - [[#433]](https://github.com/nf-core/smrnaseq/pull/433) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files.
-- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
+- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC and all modules to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
+- [[#435]](https://github.com/nf-core/smrnaseq/pull/435) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -370,14 +370,30 @@ process {
         ]
     }
 
-    withName: 'MIRTOP_COUNTS' {
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_COUNTS' {
         ext.args = '--add-extra'
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_STATS' {
+        publishDir = [ enabled: false ]
     }
 
-    withName: 'MIRTOP_GFF' {
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF' {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/mirtop/gff" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:CSVTK_JOIN' {
+        ext.args = "--fields 'UID,Read,miRNA,Variant,iso_5p,iso_3p,iso_add3p,iso_snp,iso_5p_nt,iso_3p_nt,iso_add3p_nt,iso_snp_nt' --tabs --outer-join --na \"0\" --out-delimiter \"\t\""
+        ext.prefix = "joined_samples_mirtop"
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/mirtop" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 

diff --git a/docs/output.md b/docs/output.md
@@ -140,9 +140,9 @@ If `--save_intermediates` is specified, these files will be placed in this direc
 
 **Output directory: `results/mirtop`**
 
-- `mirtop.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file
-- `mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis.
-- `mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis.
+- `gff/{sample.id}.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file
+- `joined_samples_mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis.
+- `export/{sample.id}_mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis.
 - `mirna.tsv`: tabular file with miRNA counts after summarizing unique isomiRs for each miRNA
 
 ## miRDeep2

diff --git a/modules.json b/modules.json
@@ -36,6 +36,11 @@
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
+                    "csvtk/join": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
@@ -53,22 +58,22 @@
                     },
                     "mirtop/counts": {
                         "branch": "master",
-                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
                         "installed_by": ["bam_stats_mirna_mirtop"]
                     },
                     "mirtop/export": {
                         "branch": "master",
-                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
                         "installed_by": ["bam_stats_mirna_mirtop"]
                     },
                     "mirtop/gff": {
                         "branch": "master",
-                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
                         "installed_by": ["bam_stats_mirna_mirtop"]
                     },
                     "mirtop/stats": {
                         "branch": "master",
-                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
                         "installed_by": ["bam_stats_mirna_mirtop"]
                     },
                     "mirtrace/qc": {
@@ -148,7 +153,7 @@
                     },
                     "bam_stats_mirna_mirtop": {
                         "branch": "master",
-                        "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721",
+                        "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {

diff --git a/modules/local/datatable_merge/datatable_merge.nf b/modules/local/datatable_merge/datatable_merge.nf
@@ -7,7 +7,7 @@ process TABLE_MERGE {
         'biocontainers/r-data.table:1.12.2' }"
 
     input:
-    path mirtop
+    tuple val(meta), path(mirtop)
 
     output:
     path "mirna.tsv"   , emit: mirna_tsv

diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml
diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf
diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml
diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test b/modules/nf-core/csvtk/join/tests/main.nf.test
diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test.snap b/modules/nf-core/csvtk/join/tests/main.nf.test.snap
diff --git a/modules/nf-core/csvtk/join/tests/nextflow.config b/modules/nf-core/csvtk/join/tests/nextflow.config
diff --git a/modules/nf-core/csvtk/join/tests/tags.yml b/modules/nf-core/csvtk/join/tests/tags.yml
diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml
diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf