default output

src/nanoplot/config.vsh.yaml

@@ -15,7 +15,7 @@ argument_groups:
       - name: --fastq
         type: file
         description: Data is in one or more default fastq file(s).
-        default: "src/nanoplot/test_data/test1.fastq"
+        # default: "src/nanoplot/test_data/test1.fastq"
         example: read.fq
         direction: input
         multiple: true
@@ -96,44 +96,45 @@ argument_groups:
         type: file
         description: Statistical summary from NanoPlot.
         direction: output
-        example: output/*.txt
+        default: output/*.txt
       - name: --nanoplots
         type: file
         description: Plots generated by NanoPlot.
         direction: output
-        example: output/*.png
+        default: output/*.png
       - name: --html
         type: file
         description: NanoPlot report and HTML files.
         direction: output
-        example: output/*.html
+        default: output/*.html
       - name: --log
         type: file
         description: Output Log file.
         direction: output
-        example: output/*.log
+        default: output/*.log
   - name: Options
     arguments:
-      - name: --threads
-        alternatives: [-t]
-        type: integer
-        description: Set the allowed number of threads to be used by the script.
-        example: 2
+      # - name: --threads
+      #   alternatives: [-t]
+      #   type: integer
+      #   description: Set the allowed number of threads to be used by the script.
+      #   example: 2
       - name: --verbose
         type: boolean_true
         description: Write log messages also to terminal
       - name: --store
         type: boolean_true
         description: Store the extracted data in a pickle file for future plotting.
+        # direction: output
+        # default: output/*.pickle
       - name: --raw
         type: boolean_true
         description: Store the extracted data in tab separated file.
       - name: --huge
         type: boolean_true
         description: Input data is one very large file.
       - name: --no_static
-        # type: boolean_false
-        type: boolean_true
+        type: boolean_false
         description: Do not make static (png) plots.
       - name: --prefix
         alternatives: [-p]
@@ -157,8 +158,7 @@ argument_groups:
         type: integer
         description: Drop reads shorter than length specified.
       - name: --drop_outliers
-        # type: boolean_false
-        type: boolean_true
+        type: boolean_false
         description: Drop outlier reads with extreme long length.
       - name: --downsample
         type: integer
@@ -187,8 +187,7 @@ argument_groups:
         type: boolean_true
         description: Use if you want to split the summary file by barcode.
       - name: --no_supplementary
-        # type: boolean_false
-        type: boolean_true
+        type: boolean_false
         description: Use if you want to remove supplementary alignments.
   - name: Customizing plots
     arguments:
@@ -223,8 +222,7 @@ argument_groups:
         type: boolean_true
         description: List the colormaps which are available for plotting and exit.
       - name: --no_N50 
-        # type: boolean_false
-        type: boolean_true
+        type: boolean_false
         description: Hide the N50 mark in the read length histogram.
       - name: --N50 
         type: boolean_true
@@ -239,8 +237,7 @@ argument_groups:
         type: integer
         description: Set the dpi for saving images.
       - name: --hide_stats
-        # type: boolean_false
-        type: boolean_true
+        type: boolean_false
         description: Not adding Pearson R stats in some bivariate plots.
 # Arguments not taken into account:
 #    -o, --outdir    Specify directory in which output has to be created.

src/nanoplot/script.sh

@@ -7,29 +7,31 @@ set -eo pipefail
 
 ## Default output directory
 # Search for biobox directory starting from the current working directory
-file_path=$(find "$(pwd)" -name "biobox" -type d)
-par_output="$file_path//target/result/"
+
+# file_path=$(find "$(pwd)" -name "biobox" -type d)
+# par_output="$file_path//target/result/"
+# par_output="output"
 
 # Unset flags
 [[ "$par_verbose" == "false" ]] && unset par_verbose
 [[ "$par_store" == "false" ]] && unset par_store
 [[ "$par_raw" == "false" ]] && unset par_raw
 [[ "$par_huge" == "false" ]] && unset par_huge
-[[ "$par_no_static" == "false" ]] && unset par_no_static
+[[ "$par_no_static" == "true" ]] && unset par_no_static
 [[ "$par_tsv_stats" == "false" ]] && unset par_tsv_stats
 [[ "$par_only_report" == "false" ]] && unset par_only_report
 [[ "$par_info_in_report" == "false" ]] && unset par_info_in_report
-[[ "$par_drop_outliers" == "false" ]] && unset par_drop_outliers
+[[ "$par_drop_outliers" == "true" ]] && unset par_drop_outliers
 [[ "$par_loglength" == "false" ]] && unset par_loglength
 [[ "$par_percentqual" == "false" ]] && unset par_percentqual
 [[ "$par_alength" == "false" ]] && unset par_alength
 [[ "$par_barcoded" == "false" ]] && unset par_barcoded
-[[ "$par_no_supplementary" == "false" ]] && unset par_no_supplementary
+[[ "$par_no_supplementary" == "true" ]] && unset par_no_supplementary
 [[ "$par_listcolors" == "false" ]] && unset par_listcolors
 [[ "$par_listcolormaps" == "false" ]] && unset par_listcolormaps
-[[ "$par_no_N50" == "false" ]] && unset par_no_N50
+[[ "$par_no_N50" == "true" ]] && unset par_no_N50
 [[ "$par_N50" == "false" ]] && unset par_N50
-[[ "$par_hide_stats" == "false" ]] && unset par_hide_stats
+[[ "$par_hide_stats" == "true" ]] && unset par_hide_stats
 
 # Multiple inputs - replace ';' with ' ' (space)
 par_fastq=$(echo $par_fastq | tr ';' ' ')
@@ -55,8 +57,7 @@ NanoPlot \
     ${par_cram:+--cram "$par_cram"} \
     ${par_pickle:+--pickle "$par_pickle"} \
     ${par_feather:+--feather "$par_feather"} \
-    ${par_threads:+--threads "$par_threads"} \
-    # ${meta_cpus:+--threads "${meta_cpus}"} \
+    # ${par_threads:+--threads "$par_threads"} \
     ${par_verbose:+--verbose} \
     ${par_store:+--store} \
     ${par_raw:+--raw} \
@@ -90,7 +91,8 @@ NanoPlot \
     ${par_title:+--title "$par_title"} \
     ${par_font_scale:+--font_scale "$par_font_scale"} \
     ${par_dpi:+--dpi "$par_dpi"} \
-    ${par_hide_stats:+--hide_stats}
+    ${par_hide_stats:+--hide_stats} \
+    # -o output
 
 ## Move output to output directory ##
 # Move NanoPlot summary file
@@ -100,10 +102,10 @@ if [[ -n "$par_statsum" ]]; then
     base_name=$(echo "$par_statsum" | sed 's/\*.*//')
     # Make a folder with the extracted string as the name
     mkdir -p "$base_name"
-    mv *.txt "$base_name"
-else
-    mkdir -p "$par_output"
-    mv *.txt "$par_output"
+    mv "$par_temp"/*.txt "$base_name"
+# else
+#     mkdir -p "$par_output"
+#     mv *.txt "$par_output"
 fi
 
 # Move NanoPlot plots

src/nanoplot/test.sh

@@ -102,7 +102,6 @@ echo "Test 2 succeeded."
 echo "> Run Test 3: multiple options"
 "$meta_executable" \
   --fastq "$meta_resources_dir/test_data/test1.fastq" \
-  -t 2 \
   --maxlength 40000 \
   --format jpg \
   --prefix biobox_ \

src/nanoplot/test_data/script.sh

@@ -57,9 +57,19 @@ done
 
 #########################################################################################
 
-## Bam file ##
+## Fasta file ##
+# Dowload test data from snakemake wrapper
 if [ ! -d /tmp/snakemake-wrappers ]; then
   git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
 fi
 
-cp -r /tmp/snakemake-wrappers/bio/arriba/test/A.bam src/nanoplot/test_data/test.bam
+cp -r /tmp/snakemake-wrappers/bio/assembly-stats/test/*.fasta src/nanoplot/test_data/test.fasta
+
+#########################################################################################
+
+## Bam file ##
+cp -r /tmp/snakemake-wrappers/bio/arriba/test/A.bam src/nanoplot/test_data/test.bam
+
+#########
+
+## Cram file ##