diff --git a/src/fastqc/config.vsh.yaml b/src/fastqc/config.vsh.yaml index c84f9008..97fb7c46 100644 --- a/src/fastqc/config.vsh.yaml +++ b/src/fastqc/config.vsh.yaml @@ -27,17 +27,19 @@ argument_groups: type: file direction: output multiple: true + multiple_sep: "," description: | Create an HTML report of the results. - example: report_fastqc.html + example: input_fastqc.html - name: --zip type: file direction: output multiple: true + multiple_sep: "," description: | - Create an zip file with: html report, data, images, icons etc. - example: report_fastqc.html + Create the zip file(s) containing: html report, data, images, icons etc. + example: input_fastqc.zip - name: Options arguments: diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh index 9c8a13ab..d297a414 100644 --- a/src/fastqc/script.sh +++ b/src/fastqc/script.sh @@ -12,21 +12,8 @@ [[ "$par_nogroup" == "false" ]] && unset par_nogroup [[ "$par_quiet" == "false" ]] && unset par_quiet -# if more than one file is passed -if [[ "$par_input" == *","* ]]; then - - # Retrieve the first path from the comma-separated input - par_input1=$(echo "$par_input" | cut -d',' -f1) - # Retrieve the directory of the input file - input_dir=$(dirname "$par_input1") - # Convert comma to space separated - par_input=$(echo $par_input | tr ',' ' ') - -else # if only one file is passed - # Retrives the directory of the input file - input_dir=$(dirname "$par_input") -fi -echo "input_dir: $input_dir" +# Create input array +IFS="," read -ra input <<< $par_input run fastqc fastqc \ @@ -47,20 +34,41 @@ fastqc \ ${par_kmers:+--kmers "$par_kmers"} \ ${par_quiet:+--quiet} \ ${par_dir:+--dir "$par_dir"} \ - $par_input - + ${par_input:+ ${input[*]}} +input_dir=$(dirname ${input[1]}) # Both outputs args passed if [[ -n "$par_html" ]] && [[ -n "$par_zip" ]]; then - mv "$input_dir"/*.html "$par_html" - mv "$input_dir"/*.zip "$par_zip" + IFS=',' read -r -a html_files <<< "$par_html" + IFS=',' read -r -a zip_files <<< "$par_zip" + for i in "${!input[@]}"; do + sample_name=$(basename ${input[$i]} .fq) + input_zip="$input_dir/${sample_name}_fastqc.zip" + input_html="$input_dir/${sample_name}_fastqc.html" + zip_file=${zip_files[$i]} + html_file=${html_files[$i]} + mv "$input_zip" "$zip_file" + mv "$input_html" "$html_file" + done # Only html output arg passed elif [[ -n "$par_html" ]]; then - mv "$input_dir"/*.html "$par_html" + IFS=',' read -r -a html_files <<< "$par_html" + for i in "${!input[@]}"; do + sample_name=$(basename ${input[$i]} .fq) + input_html="$input_dir/${sample_name}_fastqc.html" + html_file=${html_files[$i]} + mv "$input_html" "$html_file" + done rm "$input_dir"/*.zip # Only zip output arg passed elif [[ -n "$par_zip" ]]; then - mv "$input_dir"/*.zip "$par_zip" + IFS=',' read -r -a zip_files <<< "$par_zip" + for i in "${!input[@]}"; do + sample_name=$(basename ${input[$i]} .fq) + input_zip="$input_dir/${sample_name}_fastqc.zip" + zip_file=${zip_files[$i]} + mv "$input_zip" "$zip_file" + done rm "$input_dir"/*.html fi @@ -72,7 +80,8 @@ fi # 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! +# because this is very similar to the -outdir flag of fastqc! + # Do I create a code for the multiple files case where I also rename the files to the output args? diff --git a/src/fastqc/test_data/input_1_fastqc.html b/src/fastqc/test_data/input_1_fastqc.html new file mode 100644 index 00000000..88f23b8c --- /dev/null +++ b/src/fastqc/test_data/input_1_fastqc.html @@ -0,0 +1,187 @@ +input_1.fq FastQC Report
FastQCFastQC Report
Mon 22 Jul 2024
input_1.fq

Summary

[OK]Basic Statistics

MeasureValue
Filenameinput_1.fq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1
Sequences flagged as poor quality0
Sequence length100
%GC67

[OK]Per base sequence quality

Per base quality graph

[FAIL]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[FAIL]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[OK]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNN1100.0No Hit

[OK]Adapter Content

Adapter graph

Produced by FastQC (version 0.11.9)
\ No newline at end of file diff --git a/src/fastqc/test_data/input_1_fastqc.zip b/src/fastqc/test_data/input_1_fastqc.zip new file mode 100644 index 00000000..e4def648 Binary files /dev/null and b/src/fastqc/test_data/input_1_fastqc.zip differ diff --git a/src/fastqc/test_data/input_2_fastqc.html b/src/fastqc/test_data/input_2_fastqc.html new file mode 100644 index 00000000..dc1bcd8f --- /dev/null +++ b/src/fastqc/test_data/input_2_fastqc.html @@ -0,0 +1,187 @@ +input_2.fq FastQC Report
FastQCFastQC Report
Mon 22 Jul 2024
input_2.fq

Summary

[OK]Basic Statistics

MeasureValue
Filenameinput_2.fq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1
Sequences flagged as poor quality0
Sequence length100
%GC67

[OK]Per base sequence quality

Per base quality graph

[FAIL]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[FAIL]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[OK]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNN1100.0No Hit

[OK]Adapter Content

Adapter graph

Produced by FastQC (version 0.11.9)
\ No newline at end of file diff --git a/src/fastqc/test_data/input_2_fastqc.zip b/src/fastqc/test_data/input_2_fastqc.zip new file mode 100644 index 00000000..50124139 Binary files /dev/null and b/src/fastqc/test_data/input_2_fastqc.zip differ