Adds FASTQE for summarising FASTQ scores as emojis

nf-core · Nov 1, 2024 · 4d807e7 · 4d807e7
1 parent 5e56fc3
commit 4d807e7
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Showing 7 changed files with 362 additions and 0 deletions.
diff --git a/modules.json b/modules.json
@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "fastqe": {
+                        "branch": "master",
+                        "git_sha": "cab0b8fdc4f785810f49423d8141a0773c21eb3b",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",

diff --git a/modules/nf-core/fastqe/environment.yml b/modules/nf-core/fastqe/environment.yml
diff --git a/modules/nf-core/fastqe/main.nf b/modules/nf-core/fastqe/main.nf
diff --git a/modules/nf-core/fastqe/meta.yml b/modules/nf-core/fastqe/meta.yml
diff --git a/modules/nf-core/fastqe/tests/main.nf.test b/modules/nf-core/fastqe/tests/main.nf.test
diff --git a/modules/nf-core/fastqe/tests/main.nf.test.snap b/modules/nf-core/fastqe/tests/main.nf.test.snap
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
@@ -6,6 +6,7 @@
 
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/main'
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
+include { FASTQE                        } from '../modules/nf-core/fastqe/main'  
 
 include { MULTIQC as MULTIQC_GLOBAL     } from '../modules/nf-core/multiqc/main'
 include { MULTIQC as MULTIQC_PER_TAG    } from '../modules/nf-core/multiqc/main'
@@ -58,6 +59,15 @@ workflow SEQINSPECTOR {
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
+    // FASTQE
+    FASTQE(
+        ch_sample_sized.map {
+            meta, subsampled -> [meta, subsampled]
+        }
+    )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQE.out.tsv)
+    ch_versions = ch_versions.mix(FASTQE.out.versions.first())
+
     //
     // Collate and save software versions
     //