Commit cc3e82ed authored by khalid's avatar khalid
Browse files

typos

parent 90452403
{
id: hisat2,
name: Howtie2,
article: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).,
name: Hisat2,
article: "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).",
website: "http://daehwankimlab.github.io/hisat2/",
git: "http://daehwankimlab.github.io/hisat2/",
description: "a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)",
......@@ -90,13 +90,13 @@
],
install: {
hisat2: [
"cd /tmp"
"cd /tmp",
"wget -O hisat2-2.2.1-linux-x86_64.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download",
"unzip hisat2-2.2.1-linux-x86_64.zip",
"mv hisat2-2.2.1 /opt/biotools/",
"rm -rf hisat2-2.2.1*"
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH
"echo "export PATH=$PATH:/opt/biotools/hisat2-2.2.1" >> /etc/environment
"rm -rf hisat2-2.2.1*",
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH ",
"echo \"export PATH=$PATH:/opt/biotools/hisat2-2.2.1\" >> /etc/environment"
],
samtools: [
"cd /opt/biotools",
......
{
id: hisat2_index,
name: hisat2 index,
article: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).,
article: "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).",
website: "http://daehwankimlab.github.io/hisat2/",
git: "http://daehwankimlab.github.io/hisat2/",
description: "a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)",
......@@ -41,13 +41,13 @@
],
install: {
hisat2: [
"cd /tmp"
"cd /tmp",
"wget -O hisat2-2.2.1-linux-x86_64.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download",
"unzip hisat2-2.2.1-linux-x86_64.zip",
"mv hisat2-2.2.1 /opt/biotools/",
"rm -rf hisat2-2.2.1*"
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH
"echo "export PATH=$PATH:/opt/biotools/hisat2-2.2.1" >> /etc/environment
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH "
"echo "export PATH=$PATH:/opt/biotools/hisat2-2.2.1" >> /etc/environment"
],
},
citations: {
......
......@@ -19,6 +19,6 @@ rule <step_name>__radsex_signif:
"-o {output.significant_markers} "+
"-d {params.min_depth} " +
"--signif-threshold {params.signif_threshold}; " +
"awk -F\"\\t\" '{{ print \">\"$1\"\\n\"$2 ;}}' {output.significant_markers} > {output.significant_sequences};" +
"awk -F\"\\t\" '{{ if (NR > 2) print \">\"$1\"\\n\"$2 ;}}' {output.significant_markers} > {output.significant_sequences};" +
"awk -F\"\\t\" '{{for(i=1; i<= NF;i++) if (i != 2) printf(\"%s\\t\", $i) ; print $2 ;}}' {output.significant_markers} > {output.significant_markers}.tmp ;" +
"mv {output}.tmp {output.significant_markers}; "
"mv {output.significant_markers}.tmp {output.significant_markers}; "
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