From 3f0b672830669dafa86ca01bc75e977155ed6d19 Mon Sep 17 00:00:00 2001
From: Martin Beracochea <mbc@ebi.ac.uk>
Date: Thu, 1 Dec 2022 12:25:10 +0000
Subject: [PATCH] Update README

---
 README.md                       | 23 +++++++++++++++++++++++
 src/run.sh                      | 14 ++++++++------
 src/steps/10_restructure.sh     |  0
 src/steps/1_drep.sh             |  0
 src/steps/2_mash.sh             |  0
 src/steps/3_process_clusters.sh |  0
 src/steps/4_create_files.sh     |  0
 src/steps/4_mmseqs.sh           |  0
 src/steps/5_gtdbtk.sh           |  0
 src/steps/6_annotation.sh       |  0
 src/steps/6a_run_sanntis.sh     |  0
 src/steps/8_generate_yml.sh     |  0
 src/steps/8_post_processing.sh  |  0
 src/steps/9_databases.sh        |  0
 14 files changed, 31 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 src/run.sh
 mode change 100644 => 100755 src/steps/10_restructure.sh
 mode change 100644 => 100755 src/steps/1_drep.sh
 mode change 100644 => 100755 src/steps/2_mash.sh
 mode change 100644 => 100755 src/steps/3_process_clusters.sh
 mode change 100644 => 100755 src/steps/4_create_files.sh
 mode change 100644 => 100755 src/steps/4_mmseqs.sh
 mode change 100644 => 100755 src/steps/5_gtdbtk.sh
 mode change 100644 => 100755 src/steps/6_annotation.sh
 mode change 100644 => 100755 src/steps/6a_run_sanntis.sh
 mode change 100644 => 100755 src/steps/8_generate_yml.sh
 mode change 100644 => 100755 src/steps/8_post_processing.sh
 mode change 100644 => 100755 src/steps/9_databases.sh

diff --git a/README.md b/README.md
index 56d16e99..fbf75b18 100644
--- a/README.md
+++ b/README.md
@@ -82,4 +82,27 @@ $ bash run.sh \
 #### Example
 
 ```bash
+./run.sh \
+  -p $(pwd) \
+  -n test_catalogue \
+  -o $(pwd)/test_output \
+  -f $(pwd)/test_input \
+  -c $(pwd)/test_input/input_genomes.csv \
+  -x 1 \
+  -m 1000 \
+  -v "v1.0" \
+  -b "Test:test"
+
+==== 1. dRep steps with cwltool [/test_output/test_catalogue/scripts/step1.test_catalogue.sh] ====
+==== 2. mash2nwk submission script [/test_output/test_catalogue/scripts/step2.test_catalogue.sh] ====
+==== 3. Cluster annotation [/test_output/test_catalogue/scripts/step3.test_catalogue.sh] ====
+==== 4. mmseqs [/test_output/test_catalogue/scripts/step4.test_catalogue.sh] ====
+==== 5. GTDB-Tk [/test_output/test_catalogue/scripts/step5.test_catalogue.sh] ====
+==== 6. EggNOG, IPS, rRNA [/test_output/test_catalogue/scripts/step6.test_catalogue.sh] ====
+==== 6a. Sanntis [/test_output/test_catalogue/scripts/step6a.test_catalogue.sh] ====
+==== 7. Metadata and phylo.tree [/test_output/test_catalogue/scripts/step7.test_catalogue.sh] ====
+==== 8. Post-processing [/test_output/test_catalogue/scripts/step8.test_catalogue.sh] ====
+==== 9. Databases [/test_output/test_catalogue/scripts/step9.test_catalogue.sh] ====
+==== 10. Re-structure [/test_output/test_catalogue/scripts/step10.test_catalogue.sh] ====
+==== Final. Exit ====
 ```
\ No newline at end of file
diff --git a/src/run.sh b/src/run.sh
old mode 100644
new mode 100755
index 6e9c87e8..e6e04fce
--- a/src/run.sh
+++ b/src/run.sh
@@ -24,7 +24,6 @@ MEM_STEP5="500G"
 MEM_STEP6="50G"
 MEM_STEP6a="5G"
 MEM_STEP7="5G"
-MEM_STEP8="5G"
 MEM_STEP9="150G" # kraken needs 150G
 
 THREADS_STEP1="16"
@@ -35,7 +34,6 @@ THREADS_STEP5="32"
 THREADS_STEP6="16"
 THREADS_STEP6a="1"
 THREADS_STEP7="1"
-THREADS_STEP8="1"
 THREADS_STEP9="16"
 
 usage() {
@@ -46,6 +44,7 @@ The generated scripts will run the pipeline step by step using cwltool / toil.
 Use the -r option to generate and run the scripts (using bwait between steps).
 
 OPTIONS:
+   -p      Pipeline repo directory
    -h      Show help message
    -t      Threads. Default=4 [OPTIONAL]
    -n      Catalogue name
@@ -60,11 +59,10 @@ OPTIONS:
 EOF
 }
 
-while getopts "h:n:f:c:m:x:v:b:o:q:r" OPTION; do
+while getopts "p:n:f:c:m:x:v:b:o:q:r:h" OPTION; do
     case $OPTION in
-    h)
-        usage
-        exit 1
+    p)
+        PIPELINE_DIRECTORY=${OPTARG}
         ;;
     n)
         NAME=${OPTARG}
@@ -96,6 +94,10 @@ while getopts "h:n:f:c:m:x:v:b:o:q:r" OPTION; do
     r)
         RUN=1
         ;;
+    h)
+        usage
+        exit 1
+        ;;        
     ?)
         usage
         exit 1
diff --git a/src/steps/10_restructure.sh b/src/steps/10_restructure.sh
old mode 100644
new mode 100755
diff --git a/src/steps/1_drep.sh b/src/steps/1_drep.sh
old mode 100644
new mode 100755
diff --git a/src/steps/2_mash.sh b/src/steps/2_mash.sh
old mode 100644
new mode 100755
diff --git a/src/steps/3_process_clusters.sh b/src/steps/3_process_clusters.sh
old mode 100644
new mode 100755
diff --git a/src/steps/4_create_files.sh b/src/steps/4_create_files.sh
old mode 100644
new mode 100755
diff --git a/src/steps/4_mmseqs.sh b/src/steps/4_mmseqs.sh
old mode 100644
new mode 100755
diff --git a/src/steps/5_gtdbtk.sh b/src/steps/5_gtdbtk.sh
old mode 100644
new mode 100755
diff --git a/src/steps/6_annotation.sh b/src/steps/6_annotation.sh
old mode 100644
new mode 100755
diff --git a/src/steps/6a_run_sanntis.sh b/src/steps/6a_run_sanntis.sh
old mode 100644
new mode 100755
diff --git a/src/steps/8_generate_yml.sh b/src/steps/8_generate_yml.sh
old mode 100644
new mode 100755
diff --git a/src/steps/8_post_processing.sh b/src/steps/8_post_processing.sh
old mode 100644
new mode 100755
diff --git a/src/steps/9_databases.sh b/src/steps/9_databases.sh
old mode 100644
new mode 100755