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!"