Merge pull request #109 from vib-singlecell-nf/develop

Develop

Former-commit-id: 8c863a4

README.md

@@ -343,7 +343,7 @@ tenx {
 -profiles h5ad
 ```
 
-In the generated .config file, make sur the `file_paths` parameter is set with the paths to the `.h5ad` files:
+In the generated .config file, make sure the `file_paths` parameter is set with the paths to the `.h5ad` files:
 ```
 [...]
 h5ad {
@@ -352,10 +352,12 @@ h5ad {
 }
 [...]
 ```
-- The `suffix` parameter is used to infer the sample name from the file paths.
+- The `suffix` parameter is used to infer the sample name from the file paths (it is removed from the input file path to derive a sample name).
 - The `file_paths` accepts glob patterns and also comma separated paths.
 Make sure that `sc.file_converter.iff` is set to `h5ad`.
 
+Currently H5AD input is only implemented in the `h5ad_single_sample` entry point.
+
 ## Select the optimal number of principal components
 
 When generating the config using `nextflow config` (see above), add the `pcacv` profile.

nextflow.config

@@ -3,7 +3,7 @@ manifest {
     name = 'vib-singlecell-nf/vsn-pipelines'
     description = 'A repository of pipelines for single-cell data in Nextflow DSL2'
     homePage = 'https://github.com/vib-singlecell-nf/vsn-pipelines'
-    version = '0.8.1'
+    version = '0.8.2'
     mainScript = 'main.nf'
     defaultBranch = 'master'
     nextflowVersion = '!19.12.0-edge' // with ! prefix, stop execution if current version does not match required version.
@@ -30,6 +30,11 @@ process {
     }
 }
 
+
+includeConfig 'src/utils/conf/scope.config'
+includeConfig 'src/utils/utils.config' // utilities config
+includeConfig 'conf/generic.config'
+
 profiles {
 
     standard {
@@ -175,10 +180,6 @@ profiles {
 
 }
 
-includeConfig 'src/utils/conf/scope.config'
-includeConfig 'src/utils/utils.config' // utilities config
-includeConfig 'conf/generic.config'
-
 
 timeline {
     enabled = true

src/channels/conf/h5ad.config

@@ -2,7 +2,12 @@ params {
     data {
         h5ad {
             file_paths = ''
-            suffix = ''
+            suffix = '.h5ad'
         }
     }
+    sc {
+        file_converter {
+             iff = 'h5ad'
+         }
+     }
 }

src/utils/processes/h5adToLoom.nf

@@ -5,7 +5,7 @@ process SC__H5AD_TO_LOOM {
 
 	container params.sc.scanpy.container
 	clusterOptions "-l nodes=1:ppn=2 -l pmem=30gb -l walltime=1:00:00 -A ${params.global.qsubaccount}"
-	publishDir "${params.global.outdir}/loom", mode: 'link', overwrite: true
+    publishDir "${params.global.outdir}/loom", mode: 'link', overwrite: true, saveAs: { filename -> "${params.global.project_name}.${sampleId}.SCope_output.loom" }
 
 	input:
 		// Expects:
@@ -34,7 +34,7 @@ process SC__H5AD_TO_FILTERED_LOOM {
 
 	container params.sc.scanpy.container
 	clusterOptions "-l nodes=1:ppn=2 -l pmem=30gb -l walltime=1:00:00 -A ${params.global.qsubaccount}"
-	publishDir "${params.global.outdir}/loom", mode: 'link', overwrite: true
+    publishDir "${params.global.outdir}/data/intermediate", mode: 'symlink', overwrite: true
 
 	input:
 		tuple val(sampleId), path(f)

src/utils/processes/utils.nf

@@ -175,7 +175,7 @@ process COMPRESS_HDF5() {
 
 	container "aertslab/sctx-hdf5:1.10.5-r2"
 	clusterOptions "-l nodes=1:ppn=2 -l pmem=30gb -l walltime=1:00:00 -A ${params.global.qsubaccount}"
-	publishDir "${params.global.outdir}/loom", mode: 'link', overwrite: true
+	publishDir "${params.global.outdir}/data/intermediate", mode: 'symlink', overwrite: true
 
 	input:
 		tuple val(id), path(f)