From 1e012947e5055e133851451e8c98a8a56fda06c1 Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Thu, 22 Oct 2026 14:39:34 +0200 Subject: [PATCH] fix: stage rhog batch folders as path inputs in hog_big & hog_rest The batch folder was declared as `each rhogsrest` / `each rhogsbig`, i.e. a plain value, so Nextflow passed the absolute path as a string without staging it. Container bind mounts are derived from the staged inputs, so the folder was only visible inside the container when it happened to fall under the mounted common parent directory. --- FastOMA.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/FastOMA.nf b/FastOMA.nf index 2252849..b14c23c 100644 --- a/FastOMA.nf +++ b/FastOMA.nf @@ -201,7 +201,7 @@ process hog_big{ publishDir path: params.genetrees_folder, enabled: params.write_genetrees, pattern: "*tsv.gz" input: - each rhogsbig + each path(rhogsbig) path species_tree val nr_species @@ -243,7 +243,7 @@ process hog_rest{ publishDir path: params.genetrees_folder, enabled: params.write_genetrees, pattern: "*tsv.gz" input: - each rhogsrest + each path(rhogsrest) path species_tree output: path "pickle_hogs"