[FIX] specify container for bash-only modules for AWS

modules/local/preprocess_expdesign.nf

@@ -1,19 +1,28 @@
 // Fixing file endings only necessary if the experimental design is user-specified
+// TODO can we combine this with another step? Feels like a waste to spawn a worker for this.
+// Maybe the renaming can be done in the rawfileconversion step? Or check if the OpenMS tools
+// accept different file endings already?
 process PREPROCESS_EXPDESIGN {
     label 'process_very_low'
     label 'process_single_thread'
 
+    container "frolvlad/alpine-bash"
+
     input:
     path design
 
     output:
     path "experimental_design.tsv", emit: ch_expdesign
-    path "process_experimental_design.tsv", emit: process_ch_expdesign
+    path "config.tsv", emit: ch_config
 
     script:
 
     """
+    # since we know that we will need to convert from raw to mzML for all tools that need the design (i.e., OpenMS tools)
+    # we edit the design here and change the endings.
     sed 's/.raw\\t/.mzML\\t/I' $design > experimental_design.tsv
-    a=\$(grep -n '^\$' $design | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' $design > process_experimental_design.tsv
+
+    # here we extract the filenames and fake an empty config (since the config values will be deduced from the workflow params)
+    a=\$(grep -n '^\$' $design | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' $design > config.tsv
     """
 }

subworkflows/local/create_input_channel.nf

@@ -20,14 +20,14 @@ workflow CREATE_INPUT_CHANNEL {
     if (is_sdrf.toString().toLowerCase().contains("true")) {
         SDRFPARSING ( ch_sdrf_or_design )
         ch_versions = ch_versions.mix(SDRFPARSING.out.version)
-        ch_in_design = SDRFPARSING.out.ch_sdrf_config_file
+        ch_config = SDRFPARSING.out.ch_sdrf_config_file
 
         ch_expdesign    = SDRFPARSING.out.ch_expdesign
     } else {
         PREPROCESS_EXPDESIGN( ch_sdrf_or_design )
-        ch_in_design = PREPROCESS_EXPDESIGN.out.process_ch_expdesign
+        ch_config = PREPROCESS_EXPDESIGN.out.ch_config
 
-        ch_expdesign    = PREPROCESS_EXPDESIGN.out.ch_expdesign
+        ch_expdesign = PREPROCESS_EXPDESIGN.out.ch_expdesign
     }
 
     Set enzymes = []
@@ -38,7 +38,7 @@ workflow CREATE_INPUT_CHANNEL {
     wrapper.labelling_type = ""
     wrapper.acquisition_method = ""
 
-    ch_in_design.splitCsv(header: true, sep: '\t')
+    ch_config.splitCsv(header: true, sep: '\t')
             .map { create_meta_channel(it, is_sdrf, enzymes, files, wrapper) }
             .branch {
                 ch_meta_config_dia: it[0].acquisition_method.contains("dia")