From ba96abe8f16f38149aad8a8657aaaa6cd6e603ff Mon Sep 17 00:00:00 2001 From: "pau.piera.linde@gmail.com" Date: Mon, 7 Aug 2023 12:28:02 +0200 Subject: [PATCH] NC=0 workflow error fix --- workflow_avamb/avamb.snake.conda.smk | 2 +- .../src/write_clusters_from_dereplicated_and_ripped_bins.sh | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/workflow_avamb/avamb.snake.conda.smk b/workflow_avamb/avamb.snake.conda.smk index b30f1385..ddcbc00a 100644 --- a/workflow_avamb/avamb.snake.conda.smk +++ b/workflow_avamb/avamb.snake.conda.smk @@ -700,7 +700,7 @@ rule write_clusters_from_nc_folders: "avamb" shell: - "sh {params.path} -d {OUTDIR}/Final_bins -o {output} ;" + "sh {params.path} -d {OUTDIR}/Final_bins -o {OUTDIR} ;" "touch {log.log_fin} " # Rename and move some files and folders diff --git a/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh b/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh index 344c86bb..f8c7aa5d 100644 --- a/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh +++ b/workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh @@ -4,11 +4,12 @@ while getopts "d:o:" opt; do case $opt in d) drep_dir=$OPTARG ;; - o) clusters_file=$OPTARG ;; + o) outdir=$OPTARG ;; *) echo 'error' >&2 exit 1 esac done +clusters_file=${outdir}/avamb/avamb_manual_drep_disjoint_clusters.tsv echo 'creating z y v clusters from the final set of bins' for s in $(ls $drep_dir) do