diff --git a/src/trimgalore/config.vsh.yaml b/src/trimgalore/config.vsh.yaml index e3ca6b76..9074564e 100644 --- a/src/trimgalore/config.vsh.yaml +++ b/src/trimgalore/config.vsh.yaml @@ -236,7 +236,7 @@ argument_groups: default: trimmed_output - name: --trimmed_r1 type: file - required: true + required: false description: Output file for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: read_1.fastq @@ -248,6 +248,7 @@ argument_groups: example: read_2.fastq - name: --trimming_report_r1 type: file + required: false description: Trimming report for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: read_1.trimming_report.txt @@ -259,6 +260,7 @@ argument_groups: example: read_2.trimming_report.txt - name: --trimmed_fastqc_html_1 type: file + required: false description: FastQC report for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: read_1.fastqc.html @@ -270,6 +272,7 @@ argument_groups: example: read_2.fastqc.html - name: --trimmed_fastqc_zip_1 type: file + required: false description: FastQC results for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: read_1.fastqc.zip @@ -281,13 +284,13 @@ argument_groups: example: read_2.fastqc.zip - name: --unpaired_r1 type: file - required: true + required: false description: Output file for unpired read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: unpaired_read_1.fastq - name: --unpaired_r2 type: file - required: true + required: false description: Output file for unpaired read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists. direction: output example: unpaired_read_2.fastq