Merge pull request #38 from nf-core/feature/fastp

Add fastp and Remove dead code
nf-core · May 5, 2022 · b51f25d · b51f25d
2 parents 1a782e1 + 0eda0d3
commit b51f25d
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Showing 17 changed files with 207 additions and 448 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,8 +9,8 @@ Initial release of nf-core/demultiplex, created with the [nf-core](https://nf-co
 
 ### `Added`
 
-### `Fixed`
+- [#38](https://github.com/nf-core/demultiplex/pull/388) - Add FastP
 
-### `Dependencies`
+### `Fixed`
 
 ### `Deprecated`
diff --git a/modules.json b/modules.json
@@ -3,12 +3,12 @@
     "homePage": "https://github.com/nf-core/demultiplex",
     "repos": {
         "nf-core/modules": {
-            "cellranger/mkfastq": {
-                "git_sha": "f0800157544a82ae222931764483331a81812012"
-            },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "fastp": {
+                "git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
+            },
             "multiqc": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
             },

diff --git a/modules/local/bcl2fastq.nf b/modules/local/bcl2fastq.nf
diff --git a/modules/local/bcl2fastq_problem_ss.nf b/modules/local/bcl2fastq_problem_ss.nf
diff --git a/modules/local/bclconvert/main.nf b/modules/local/bclconvert/main.nf
@@ -15,9 +15,9 @@ process BCLCONVERT {
     tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz")           ,optional:true ,emit: fastq_idx
     tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,emit: undetermined
     tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx
-    path("Reports/*.{csv,xml}")                                   ,emit: reports
-    path("Logs/*.{log,txt}")                                      ,emit: logs
-    path("**.bin")                                                ,emit: interop
+    tuple val(meta), path("Reports/*.{csv,xml}")                  ,emit: reports
+    tuple val(meta), path("Logs/*.{log,txt}")                     ,emit: logs
+    tuple val(meta), path("**.bin")                               ,emit: interop
     path("versions.yml")                                          ,emit: versions
 
     when:

diff --git a/modules/local/fastq_screen.nf b/modules/local/fastq_screen.nf
diff --git a/modules/local/make_fake_ss.nf b/modules/local/make_fake_ss.nf
diff --git a/modules/local/parse_jsonfile.nf b/modules/local/parse_jsonfile.nf
diff --git a/modules/local/recheck_samplesheet.nf b/modules/local/recheck_samplesheet.nf
diff --git a/modules/local/reformat_samplesheet.nf b/modules/local/reformat_samplesheet.nf
diff --git a/modules/nf-core/modules/cellranger/mkfastq/Dockerfile b/modules/nf-core/modules/cellranger/mkfastq/Dockerfile
diff --git a/modules/nf-core/modules/cellranger/mkfastq/README.md b/modules/nf-core/modules/cellranger/mkfastq/README.md