Small Changes

src/fastqc/config.vsh.yaml

@@ -35,6 +35,7 @@ argument_groups:
       - name: --zip
         type: file
         direction: output
+        multiple: true
         multiple_sep: ","
         description: |
           Create the zip file(s) containing: html report, data, images, icons etc.
@@ -45,18 +46,33 @@ argument_groups:
         type: file
         direction: output
         description: |
-          Create the output files in the specified directory.
+          Create all output files in the specified output directory.
+          Please note that this directory must exist as the program
+          will not create it.  If this option is not set then the 
+          output file for each sequence file is created in the same
+          directory as the sequence file which was processed.
         example: output_dir
 
   - name: Options
     arguments:  
       - name: --casava
         type: boolean_true
-        description: Files come from raw casava output.
+        description: | 
+          Files come from raw casava output. Files in the same sample
+          group (differing only by the group number) will be analysed
+          as a set rather than individually. Sequences with the filter
+          flag set in the header will be excluded from the analysis.
+          Files must have the same names given to them by casava
+          (including being gzipped and ending with .gz) otherwise they
+          won't be grouped together correctly.
       
       - name: --nano
         type: boolean_true
-        description: Files come from nanopore sequences and are in fast5 format.
+        description: |
+          Files come from nanopore sequences and are in fast5 format. In
+          this mode you can pass in directories to process and the program
+          will take in all fast5 files within those directories and produce
+          a single output file from the sequences found in all files.
       
       - name: --nofilter
         type: boolean_true
@@ -184,7 +200,6 @@ argument_groups:
           files written when generating report images. 
           Defaults to system temp directory if not specified.
         example: temp_dir
-
 
 
 resources:

src/fastqc/script.sh

@@ -37,8 +37,6 @@ fastqc \
   ${par_input:+ ${input[*]}}
 
 input_dir=$(dirname ${input[0]})
-# echo "input dir: $input_dir"
-# echo "input: ${input[*]}"
 
 # Both outputs args passed
 if [[ -n "$par_html" ]] && [[ -n "$par_zip" ]]; then
@@ -77,17 +75,15 @@ fi
 
 
 # Questions:
-# Should I unzip the zip file output and make multiple other outputs options for the viash component?
-# TODO: handle the output args if multiple files are passed
-# - if multiple files are passed, for the output args I can either change the config to multiple=false 
-# and pass just a dir as argument and mv the files to this dir, 
-# and would also work as well in the case of just one file passed (rename would be possible).
-# i guess I can discuss this with jakub and see what he thinks is best
-# because this is very similar to the -outdir flag of fastqc!
+# multiple = true does not allow for output without a * in the name. In the output.
+# Do I create output args for the unzip files?
 
-# Do I create a code for the multiple files case where I also rename the files to the output args?
 
 
+
+# echo "zip files: ${zip_files[*]}"
+# echo "input files: ${input[*]}"
+# pwd
 #[[ -z "$par_java" ]] && unset par_java
 #[[ "$par_min_length" == "false" ]] && unset par_min_length
 #[[ "$par_format" == "false" ]] && unset par_format