From 07394055e6e52b0628d9e23da111978e38b3521b Mon Sep 17 00:00:00 2001
From: Ammar <spidermine63@gmail.com>
Date: Thu, 19 May 2022 15:21:59 +1000
Subject: [PATCH] minor update v0.3.77

---
 .github/workflows/zip_release.yml | 2 +-
 snakefile                         | 6 +++---
 tools/auto_install.sh             | 9 +++++----
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/zip_release.yml b/.github/workflows/zip_release.yml
index 642900b..c9ce569 100644
--- a/.github/workflows/zip_release.yml
+++ b/.github/workflows/zip_release.yml
@@ -15,7 +15,7 @@ jobs:
       with:
         type: 'tar'
         filename: 'latest.tar.gz'
-        exclusions: '*.git* .'
+        exclusions: '*.git* . latest.tar.gz'
     - name: Upload Release
       uses: ncipollo/release-action@v1
       with:
diff --git a/snakefile b/snakefile
index e7200ff..ae6a220 100755
--- a/snakefile
+++ b/snakefile
@@ -135,7 +135,7 @@ if run_mode == 'single':
 ## Trimming ---------------------------------------------------------------------
 if trim_prog not in ['standard', 'tile']:
     sys.exit("Configuration incorrect, check 'trim_prog' it must be: standard or tile")
-if trim_org not in ['h1', 'h3']:
+if trim_org not in ['h1', 'h3', '']:
     sys.exit("Configuration incorrect, check 'trim_org' it must be: h1 or h3. bvic is not supported")
 
 if org == 'FLU':
@@ -199,8 +199,8 @@ if run_mode == 'paired':
                 R2_out_right = workspace + "qualtrim/{sample}.R2.fastq",
                 status = workspace + "status/filter_{sample}.txt"
             params:
-               Fadapter = f"bin/adapters/{org}_tile_left_{trim_org}.fa",
-               Radapter = f"bin/adapters/{org}_tile_right_{trim_org}.fa",
+               Fadapter = f"bin/adapters/{org}{trim_org}_tile_left.fa",
+               Radapter = f"bin/adapters/{org}{trim_org}_tile_right.fa",
                stats1 = workspace + "logs/trimStats1_{sample}.txt",
                stats2 = workspace + "logs/trimStats2_{sample}.txt",
                refstats1 = workspace + "logs/trimRefStats1_{sample}.txt",
diff --git a/tools/auto_install.sh b/tools/auto_install.sh
index 7ea2303..03ab854 100755
--- a/tools/auto_install.sh
+++ b/tools/auto_install.sh
@@ -224,7 +224,7 @@ status 'Installing wfi'
 message 'Attempting to download latest release of wfi'
 LATEST_URL=$(curl -s https://api.github.com/repos/ammaraziz/wfi/releases | grep "browser_download_url" | cut -d '"' -f 4 | head -n 1)
 NAME_WFI=$(basename $LATEST_URL)
-DIR_WFI=$PREFIX/${NAME_WFI/.tar.gz/}
+
 
 wget -q $LATEST_URL -P $PREFIX
 if [[ $? -ne 0 ]]; then
@@ -233,9 +233,10 @@ if [[ $? -ne 0 ]]; then
 fi
 message 'Latest version downloaded, attempting to uncompress and setup wfi pipline.'
 
-tar -xf $PREFIX/$NAME_WFI
-unzip -q $DIR_WFI/bin/flu-amd.zip -d $DIR_WFI/bin/
-bash $DIR_WFI/tools/mod_init.sh -i $DIR_WFI/bin/flu-amd/IRMA_RES/modules/FLU/init.sh
+mkdir wfi_latest
+tar -xf $PREFIX/$NAME_WFI -C wfi_latest
+unzip -q wfi_latest/bin/flu-amd.zip -d wfi_latest/bin/
+bash wfi_latest/tools/mod_init.sh -i wfi_latest/bin/flu-amd/IRMA_RES/modules/FLU/init.sh
 
 message "wfi has finished installing!"