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commit 41a2cbad0bba5915f2a0caf25daddd0d7d22c27b Author: Andreas Tille <[email protected]> Date: Wed Nov 30 08:28:16 2016 +0100 Add manpage --- debian/control | 2 +- debian/manpages | 1 + debian/qcumber.1 | 105 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 107 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index db1cbeb..6c96917 100644 --- a/debian/control +++ b/debian/control @@ -35,7 +35,7 @@ Conflicts: qc-pipeline Provides: qc-pipeline Replaces: qc-pipeline Description: quality control of genomic sequences - QCPipeline is a tool for quality control. The workflow is as followed: + QCPipeline is a tool for quality control. The workflow is as follows: . 1. Quality control with FastQC 2. Trim Reads with Trimmomatic diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 diff --git a/debian/qcumber.1 b/debian/qcumber.1 new file mode 100644 index 0000000..33d5156 --- /dev/null +++ b/debian/qcumber.1 @@ -0,0 +1,105 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. +.TH QCUMBER "1" "November 2016" "qcumber 1.0.1" "User Commands" +.SH NAME +qcumber \- quality control of genomic sequences +.SH SYNOPSIS +.Bqcumber + [\-h] [\-input INPUT] [\-1 R1] [\-2 R2] [\-output OUTPUT] +\fB\-technology\fR {Illumina,IonTorrent} [\-threads THREADS] +[\-adapter {TruSeq2\-PE,TruSeq2\-SE,TruSeq3\-PE,TruSeq3\-SE,TruSeq3\-PE\-2,NexteraPE\-PE}] +[\-reference REFERENCE] [\-index INDEX] [\-sav SAV] +[\-save_mapping] [\-db DB] [\-palindrome PALINDROME] +[\-minlen MINLEN] [\-trimOption TRIMOPTION] [\-version] +[\-nokraken] [\-nomapping] [\-trimBetter] +[\-trimBetter_threshold TRIMBETTER_THRESHOLD] [\-forAssembly] +[\-forMapping] +.SH DESCRIPTION +QCPipeline is a tool for quality control. The workflow is as follows: +.nr step 1 1 +.IP \n[step] 3 +Quality control with FastQC +.IP \n+[step] +Trim Reads with Trimmomatic +.IP \n+[step] +Quality control of trimmed reads with FastQC +.IP \n+[step] +Map reads against reference using bowtie2 +.IP \n+[step] +Classify reads with Kraken +.SH OPTIONS +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-input\fR INPUT +input sample folder. Illumina filenames have to end +with _<lane>_<R1|R2>_number, e.g. +Sample_12_345_R1_001.fastq +.TP +\fB\-1\fR R1 +input file. Illumina filename must not match +<project>_<lane>_<R1|R2>_<number> name pattern +.TP +\fB\-2\fR R2 +input file +.HP +\fB\-output\fR OUTPUT +.HP +\fB\-technology\fR {Illumina,IonTorrent} +.HP +\fB\-threads\fR THREADS +.HP +\fB\-adapter\fR {TruSeq2\-PE,TruSeq2\-SE,TruSeq3\-PE,TruSeq3\-SE,TruSeq3\-PE\-2,NexteraPE\-PE} +.TP +\fB\-reference\fR REFERENCE +Map reads against reference +.TP +\fB\-index\fR INDEX +Bowtie2 index if available. +.TP +\fB\-sav\fR SAV +Illumina folder for SAV. Requires RunInfo.xml, +RunParamter.xml and Interop folder. +.HP +\fB\-save_mapping\fR +.TP +\fB\-db\fR DB +Kraken database +.TP +\fB\-palindrome\fR PALINDROME +Use palindrome parameter 30 or 1000 for further +analysis. Default:30 +.TP +\fB\-minlen\fR MINLEN +Minlen parameter for Trimmomatic. Default:50 +.TP +\fB\-trimOption\fR TRIMOPTION +Use maxinfo or slidinginfo for +Trimmomatic.MAXINFO:<target length>:<strictness> | +SLIDINGWINDOW:<window size>:<required quality>. +default: SLIDINGWINDOW:4:15 +.TP +\fB\-version\fR +show program's version number and exit +.HP +\fB\-nokraken\fR +.HP +\fB\-nomapping\fR +.TP +\fB\-trimBetter\fR +Optimize trimming parameter using 'Per sequence base +content' from fastqc. Not recommended for amplicons. +.TP +\fB\-trimBetter_threshold\fR TRIMBETTER_THRESHOLD +Set \fB\-trimBetter\fR to use this option.Default setting for +Illumina: 0.15 and for IonTorrent: 0.25. +.TP +\fB\-forAssembly\fR +Set \fB\-trimBetter\fR to use this option.Trim parameter are +optimized for assemblies (trim more aggressive). +.TP +\fB\-forMapping\fR +Set \fB\-trimBetter\fR to use this option.Trim parameter are +optimized for mapping (allow more errors). +.SH AUTHOR +This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qcumber.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
