adapt WDs..

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
 

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
 

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
 

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
 

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
 ```

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
 

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"

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"
 

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"