Merge pull request #332 from danilodileo/modified-tree-structure

Modified tree structure
nf-core · Feb 11, 2025 · 18886a5 · 18886a5
2 parents da272d0 + 72826b0
commit 18886a5
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Showing 110 changed files with 1,395 additions and 296 deletions.
diff --git a/modules.json b/modules.json
@@ -7,62 +7,62 @@
                 "nf-core": {
                     "bbmap/align": {
                         "branch": "master",
-                        "git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbnorm": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "bbmap/index": {
                         "branch": "master",
-                        "git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "pigz/compress": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
@@ -92,33 +92,33 @@
                     },
                     "seqtk/mergepe": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "seqtk/seq": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "spades": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "9508616bf800acc767de4678d6b86cfcb27b9aeb",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "taxonkit/lineage": {
                         "branch": "master",
-                        "git_sha": "90c5156bfa6326edadbeff4a1ca196c6d10fd2ec",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/taxonkit/lineage/taxonkit-lineage.diff"
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "8d3e71002c5008e3f68a691ad8cd32c346356258",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/cat/cat_contigs.nf b/modules/local/cat/cat_contigs.nf
diff --git a/modules/local/cat/cat_db.nf b/modules/local/cat/cat_db.nf
diff --git a/modules/local/cat/cat_db_generate.nf b/modules/local/cat/cat_db_generate.nf
diff --git a/modules/local/cat/cat_summary.nf b/modules/local/cat/cat_summary.nf
diff --git a/modules/local/collect/featurecounts/environment.yml b/modules/local/collect/featurecounts/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
diff --git a/modules/local/collect_featurecounts.nf → modules/local/collect/featurecounts/main.nf b/modules/local/collect_featurecounts.nf → modules/local/collect/featurecounts/main.nf
@@ -2,7 +2,7 @@ process COLLECT_FEATURECOUNTS {
     tag "$meta.id"
     label 'process_high'
 
-    conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
         'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

diff --git a/modules/local/collect/featurecounts/meta.yml b/modules/local/collect/featurecounts/meta.yml
@@ -0,0 +1,31 @@
+name: "collect_featurecounts"
+description: Collects and processes featureCounts output files
+keywords:
+  - featurecounts
+  - collect
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - inputfiles:
+      type: file
+      description: Input featureCounts TSV files
+      pattern: "*.featureCounts.tsv"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - counts:
+      type: file
+      description: Processed counts TSV file
+      pattern: "*.counts.tsv.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@danilodileo"
diff --git a/modules/local/collect/stats/environment.yml b/modules/local/collect/stats/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
diff --git a/modules/local/collect_stats.nf → modules/local/collect/stats/main.nf b/modules/local/collect_stats.nf → modules/local/collect/stats/main.nf
@@ -2,7 +2,7 @@ process COLLECT_STATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
         'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

diff --git a/modules/local/collect/stats/meta.yml b/modules/local/collect/stats/meta.yml
@@ -0,0 +1,45 @@
+name: "collect_stats"
+description: Collects and processes various statistics from different analysis steps
+keywords:
+  - stats
+  - collect
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - samples:
+      type: value
+      description: List of sample names
+  - trimlogs:
+      type: file
+      description: Trimming log files
+      pattern: "*.trimming_report.txt"
+  - bblogs:
+      type: file
+      description: BBDuk log files
+      pattern: "*.bbduk.log"
+  - idxstats:
+      type: file
+      description: SAMtools idxstats output files
+      pattern: "*.idxstats"
+  - fcs:
+      type: file
+      description: Feature counts output file
+      pattern: "*.featureCounts.tsv"
+  - mergetab:
+      type: file
+      description: Merged taxonomy and function statistics file (optional)
+      pattern: "*.tsv"
+output:
+  - overall_stats:
+      type: file
+      description: Compiled overall statistics file
+      pattern: "*.overall_stats.tsv.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@danilodileo"
diff --git a/modules/local/diamond/blastp/environment.yml b/modules/local/diamond/blastp/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "diamond:2.1.10"
diff --git a/modules/local/diamond/blastp.nf → modules/local/diamond/blastp/main.nf b/modules/local/diamond/blastp.nf → modules/local/diamond/blastp/main.nf