From 4c88a8d4b57247c46eaaa2f2c79a7a57ac12e65e Mon Sep 17 00:00:00 2001 From: Dominik <dominik.brilhaus@hhu.de> Date: Fri, 26 Aug 2022 10:57:25 +0200 Subject: [PATCH] adapt WDs.. --- runs/kallisto_collect/README.md | 2 +- runs/kallisto_index/README.md | 2 +- runs/kallisto_quant/README.md | 2 +- runs/kallisto_sleuth/README.md | 2 +- runs/merged_isa_metadata/README.md | 4 ++-- runs/shiny_prep/README.md | 2 +- workflows/kallisto_collect/kallisto_collect.R | 2 +- workflows/kallisto_sleuth/kallisto_sleuth.R | 2 +- workflows/shiny_prep/shiny_prep.R | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md index b43b9ca..644698a 100644 --- a/runs/kallisto_collect/README.md +++ b/runs/kallisto_collect/README.md @@ -3,7 +3,7 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_collect +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_collect ## Let it flow diff --git a/runs/kallisto_index/README.md b/runs/kallisto_index/README.md index 577a1e4..2271f59 100644 --- a/runs/kallisto_index/README.md +++ b/runs/kallisto_index/README.md @@ -3,7 +3,7 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_index +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_index ## Let it flow diff --git a/runs/kallisto_quant/README.md b/runs/kallisto_quant/README.md index 34ee542..b3a3ac8 100644 --- a/runs/kallisto_quant/README.md +++ b/runs/kallisto_quant/README.md @@ -3,7 +3,7 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_quant ## Let it flow diff --git a/runs/kallisto_sleuth/README.md b/runs/kallisto_sleuth/README.md index 9df2ee4..ade0a1e 100644 --- a/runs/kallisto_sleuth/README.md +++ b/runs/kallisto_sleuth/README.md @@ -3,7 +3,7 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_sleuth ## Let it flow diff --git a/runs/merged_isa_metadata/README.md b/runs/merged_isa_metadata/README.md index 3f48961..d15e984 100644 --- a/runs/merged_isa_metadata/README.md +++ b/runs/merged_isa_metadata/README.md @@ -3,12 +3,12 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/merged_isa_metadata +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/merged_isa_metadata ## Let it flow ```bash ### run with cwltool -cwltool --enable-dev run.cwl merge_isa_metadata.yml +cwltool run.cwl merge_isa_metadata.yml ``` diff --git a/runs/shiny_prep/README.md b/runs/shiny_prep/README.md index e965857..d27503b 100644 --- a/runs/shiny_prep/README.md +++ b/runs/shiny_prep/README.md @@ -3,7 +3,7 @@ ## First cd into the (runs) folder, with the .yml file -cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_sleuth +cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq_adrian/runs/kallisto_sleuth ## Let it flow diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R index 15e176c..6c221c2 100644 --- a/workflows/kallisto_collect/kallisto_collect.R +++ b/workflows/kallisto_collect/kallisto_collect.R @@ -4,7 +4,7 @@ #### CWL-independent tests ################################################ -# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/" +# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/" # in_kallisto_results <- "runs/kallisto_quant/kallisto_results" # in_metadata_file <- "runs/merged_isa_metadata/merged_isa.tsv" # in_metadata_sample <- "Sample.Name.2" diff --git a/workflows/kallisto_sleuth/kallisto_sleuth.R b/workflows/kallisto_sleuth/kallisto_sleuth.R index e4c895e..688904d 100644 --- a/workflows/kallisto_sleuth/kallisto_sleuth.R +++ b/workflows/kallisto_sleuth/kallisto_sleuth.R @@ -7,7 +7,7 @@ #### CWL-independent tests ################################################ -# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/" +# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/" # in_sleuth <- "runs/kallisto_collect/kallisto_sleuthObject.RData" # out_folder <- "runs/kallisto_sleuth" diff --git a/workflows/shiny_prep/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R index c46afba..07c4465 100644 --- a/workflows/shiny_prep/shiny_prep.R +++ b/workflows/shiny_prep/shiny_prep.R @@ -4,7 +4,7 @@ #### CWL-independent tests ################################################ -# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq/" +# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/" # out_folder <- "runs/shiny_prep" # in_kallisto_df <- "runs/kallisto_collect/kallisto_df.csv" -- GitLab