diff --git a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh index 422e836..a73f9af 100755 --- a/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh +++ b/packages/2023_Salazar_MachuPicchu/2023_Salazar_MachuPicchu.tsv_patch.sh @@ -2,7 +2,7 @@ set -uo pipefail ## Pipefail, complain on new unassigned variables. ## Track the version of the TSV_patch template used -VERSION='0.2.0dev' +VERSION='0.2.1dev' ## This script is applied to the eager input TSV file locally to edit the dummy ## path to the fastQ files added by `create_eager_input.sh` to a real local @@ -10,13 +10,13 @@ VERSION='0.2.0dev' ## TSV before running eager should be added below that in the form of bash ## commands to aid in reproducibility. -## usage tsv_patch.sh +## usage tsv_patch.sh local_data_dir="$(readlink -f ${1})" input_tsv="$(readlink -f ${2})" output_tsv="$(dirname ${local_data_dir})/$(basename -s ".tsv" ${input_tsv}).finalised.tsv" columns_to_keep=("Sample_Name" "Library_ID" "Lane" "Colour_Chemistry" "SeqType" "Organism" "Strandedness" "UDG_Treatment" "R1" "R2" "BAM") -source $(dirname ${2})/../../scripts/source_me.sh ## Load helper functions +source $(readlink -f ${3}) ## Path to helper function script should be provided as 3rd argument. https://github.com/poseidon-framework/poseidon-eager/blob/main/scripts/source_me.sh ## Index non-proliferated columns and exclude them from the finalised TSV cut_selector=''