Merge pull request #16 from ATpoint/dev

v2.2
ATpoint · Jul 23, 2023 · c90541b · c90541b
2 parents b7fe502 + 70d655d
commit c90541b
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Showing 6 changed files with 87 additions and 53 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # atac_chip_preprocess
 
+# v2.2
+- trim process will now always output fastp report regardless of `--keep_trim`
+- improve documentation
+
 # v2.1
 - input is now a samplesheet indicating sample name and the R1/R2 files plus a group information.
 - separated trimming and alignment/sort into separate processes
@@ -18,4 +22,4 @@
 - remove the conda CI test, only run with Docker
 
 ## < 2.0
-(...)
+(...)
diff --git a/README.md b/README.md
diff --git a/bin/validate_samplesheet.R b/bin/validate_samplesheet.R
@@ -13,7 +13,6 @@ if(length_ss != 3 | sum_ss != 3)
 unique_sample <- unique(ss$sample)
 for(u in unique_sample){
 
-  # Libtype for same sample must be identical
   sx <- ss[ss$sample==u,]
 
   # R1 and R2 must not have duplicates

diff --git a/environment.yml b/environment.yml
@@ -20,5 +20,3 @@ dependencies:
   - tabix
   - ucsc-bedgraphtobigwig
   - ucsc-bigwigtobedgraph
-
-
diff --git a/modules/cat_fastq.nf b/modules/cat_fastq.nf
@@ -12,7 +12,9 @@ process CatFastq {
     publishDir = [
         path: params.outdir,
         mode: params.publishmode,
-        saveAs: { filename -> !(filename.endsWith("fq.gz") & params.keep) || filename.equals("versions.txt") || filename.equals("command_lines.txt") ? null : filename } 
+        saveAs: { filename -> 
+            (filename.endsWith("fq.gz") & params.keep) ? filename : null
+        } 
     ]
 
     container params.container

diff --git a/modules/trim.nf b/modules/trim.nf
@@ -11,7 +11,11 @@ process Trim {
     publishDir = [
         path: params.outdir,
         mode: params.publishmode,
-        saveAs: { filename -> !(filename.endsWith("fq.gz") & params.keep) || filename.equals("versions.txt") || filename.equals("command_lines.txt") ? null : filename } 
+        saveAs: { filename -> 
+            (filename.endsWith("fq.gz") & params.keep) || 
+            (filename.endsWith(".html")) ||
+            (filename.endsWith(".json")) ? filename : null
+        }
     ]
 
     container params.container
Original file line number	Diff line number	Diff line change
Expand Up		@@ -20,5 +20,3 @@ dependencies:
		- tabix
		- ucsc-bedgraphtobigwig
		- ucsc-bigwigtobedgraph