From 8e1a72aeeda516cec4429c104c024d5a5997f4b1 Mon Sep 17 00:00:00 2001 From: Hendrik Cannoodt Date: Fri, 27 Sep 2024 11:09:17 +0200 Subject: [PATCH 1/3] Fixes the typo raised in issue #132 --- src/falco/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml index de9906ef..e4d289de 100644 --- a/src/falco/config.vsh.yaml +++ b/src/falco/config.vsh.yaml @@ -86,7 +86,7 @@ argument_groups: bisulfite sequencing, and more Ts and fewer Cs are therefore expected and will be accounted for in base content. - - name: --reverse_complliment + - name: --reverse_compliment alternatives: [-r] type: boolean_true description: | From 7cf018e14e5886ced0a3f05f8f5d169a558959dc Mon Sep 17 00:00:00 2001 From: Hendrik Cannoodt Date: Fri, 27 Sep 2024 11:17:02 +0200 Subject: [PATCH 2/3] Add changelog entry --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0613fa25..290abc27 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,10 @@ * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93). +## BREAKING CHANGES + +* `falco`: Fix a typo in the `--reverse_compliment` argument (PR #157). + ## MINOR CHANGES * Upgrade to Viash 0.9.0. From 63342446418c953650f4ab2ab664821b7ed9c097 Mon Sep 17 00:00:00 2001 From: jakubmajercik Date: Fri, 27 Sep 2024 11:51:15 +0200 Subject: [PATCH 3/3] fix typo, modify script --- CHANGELOG.md | 2 +- src/falco/config.vsh.yaml | 2 +- src/falco/script.sh | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 290abc27..a2aa5387 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ ## BREAKING CHANGES -* `falco`: Fix a typo in the `--reverse_compliment` argument (PR #157). +* `falco`: Fix a typo in the `--reverse_complement` argument (PR #157). ## MINOR CHANGES diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml index e4d289de..a161e252 100644 --- a/src/falco/config.vsh.yaml +++ b/src/falco/config.vsh.yaml @@ -86,7 +86,7 @@ argument_groups: bisulfite sequencing, and more Ts and fewer Cs are therefore expected and will be accounted for in base content. - - name: --reverse_compliment + - name: --reverse_complement alternatives: [-r] type: boolean_true description: | diff --git a/src/falco/script.sh b/src/falco/script.sh index 43f5efe5..13e2eab4 100644 --- a/src/falco/script.sh +++ b/src/falco/script.sh @@ -4,7 +4,7 @@ set -eo pipefail [[ "$par_nogroup" == "false" ]] && unset par_nogroup [[ "$par_bisulfite" == "false" ]] && unset par_bisulfite -[[ "$par_reverse_compliment" == "false" ]] && unset par_reverse_compliment +[[ "$par_reverse_complement" == "false" ]] && unset par_reverse_complement IFS=";" read -ra input <<< $par_input @@ -15,7 +15,7 @@ $(which falco) \ ${par_limits:+--limits "$par_limits"} \ ${par_subsample:+-subsample $par_subsample} \ ${par_bisulfite:+-bisulfite} \ - ${par_reverse_compliment:+-reverse-compliment} \ + ${par_reverse_complement:+-reverse-complement} \ ${par_outdir:+--outdir "$par_outdir"} \ ${par_format:+--format "$par_format"} \ ${par_data_filename:+-data-filename "$par_data_filename"} \