[med-svn] [Git][med-team/bcl2fastq2][master] Add manpage

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / bcl2fastq2


Commits:
4c9e9ee4 by Andreas Tille at 2018-03-17T00:12:51+01:00
Add manpage

- - - - -


2 changed files:

- + debian/bcl2fastq.1
- + debian/createmanpages


Changes:

=====================================
debian/bcl2fastq.1
=====================================
--- /dev/null
+++ b/debian/bcl2fastq.1
@@ -0,0 +1,172 @@
+.TH BCL2FASTQ "1" "June 2017" "bcl2fastq 2.19.1.403" "User Commands"
+.SH NAME
+bcl2fastq \- BCL to FASTQ file converter
+.SH SYNOPSIS
+.B bcl2fastq
+\fB[options]\fR
+.SH DESCRIPTION
+The bcl2fastq2 Conversion Software can be used to convert BCL files from
+MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems. For conversion
+of data generated on Illumina sequencing systems using versions of RTA
+earlier than RTA 1.18.54, use bcl2fastq v1.8.4.
+.SH OPTIONS
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+produce help message and exit
+.TP
+\fB\-v\fR [ \fB\-\-version\fR ]
+print program version
+information
+.TP
+\fB\-l\fR [ \fB\-\-min\-log\-level\fR ] arg (=INFO)
+minimum log level
+recognized values: NONE,
+FATAL, ERROR, WARNING, INFO,
+DEBUG, TRACE
+.TP
+\fB\-i\fR [ \fB\-\-input\-dir\fR ] arg (=<runfolder\-dir>/Data/Intensities/BaseCalls/)
+path to input directory
+.TP
+\fB\-R\fR [ \fB\-\-runfolder\-dir\fR ] arg (=./)
+path to runfolder directory
+.TP
+\fB\-\-intensities\-dir\fR arg (=<input\-dir>/../)
+path to intensities directory
+If intensities directory is
+specified, \fB\-\-input\-dir\fR must
+also be specified.
+.TP
+\fB\-o\fR [ \fB\-\-output\-dir\fR ] arg (=<input\-dir>)
+path to demultiplexed output
+.TP
+\fB\-\-interop\-dir\fR arg (=<runfolder\-dir>/InterOp/)
+path to demultiplexing
+statistics directory
+.TP
+\fB\-\-stats\-dir\fR arg (=<output\-dir>/Stats/)
+path to human\-readable
+demultiplexing statistics
+directory
+.TP
+\fB\-\-reports\-dir\fR arg (=<output\-dir>/Reports/)
+path to reporting directory
+.TP
+\fB\-\-sample\-sheet\fR arg (=<runfolder\-dir>/SampleSheet.csv)
+path to the sample sheet
+.TP
+\fB\-r\fR [ \fB\-\-loading\-threads\fR ] arg (=4)
+number of threads used for
+loading BCL data
+.TP
+\fB\-p\fR [ \fB\-\-processing\-threads\fR ] arg
+number of threads used for
+processing demultiplexed data
+.TP
+\fB\-w\fR [ \fB\-\-writing\-threads\fR ] arg (=4)
+number of threads used for
+writing FASTQ data.
+This should not be set higher
+than the number of samples.
+If set =0 then these threads
+will be placed in the same
+pool as the loading threads,
+and the number of shared
+threads will be determined by
+\fB\-\-loading\-threads\fR.
+.TP
+\fB\-\-tiles\fR arg
+comma\-separated list of
+regular expressions to select
+only a subset of the tiles
+available in the flow\-cell.
+Multiple entries allowed,
+each applies to the
+corresponding base\-calls.
+For example:
+.TP
+* to select all the tiles
+ending with '5' in all lanes:
+.TP
+\fB\-\-tiles\fR [0\-9][0\-9][0\-9]5
+* to select tile 2 in lane 1
+.TP
+and all the tiles in the
+other lanes:
+.IP
+\fB\-\-tiles\fR s_1_0002,s_[2\-8]
+.TP
+\fB\-\-minimum\-trimmed\-read\-length\fR arg (=35)
+minimum read length after
+adapter trimming
+.TP
+\fB\-\-use\-bases\-mask\fR arg
+specifies how to use each
+cycle.
+.TP
+\fB\-\-mask\-short\-adapter\-reads\fR arg (=22)
+smallest number of remaining
+bases (after masking bases
+below the minimum trimmed
+read length) below which
+whole read is masked
+.TP
+\fB\-\-adapter\-stringency\fR arg (=0.9)
+adapter stringency
+.TP
+\fB\-\-ignore\-missing\-bcls\fR
+assume 'N'/'#' for missing
+calls
+.TP
+\fB\-\-ignore\-missing\-filter\fR
+assume 'true' for missing
+filters
+.TP
+\fB\-\-ignore\-missing\-positions\fR
+assume [0,i] for missing
+positions, where i is
+incremented starting from 0
+.TP
+\fB\-\-ignore\-missing\-controls\fR
+(deprecated) assume 0 for
+missing controls
+.TP
+\fB\-\-write\-fastq\-reverse\-complement\fR
+generate FASTQs containing
+reverse complements of actual
+data
+.TP
+\fB\-\-with\-failed\-reads\fR
+include non\-PF clusters
+.TP
+\fB\-\-create\-fastq\-for\-index\-reads\fR
+create FASTQ files also for
+index reads
+.TP
+\fB\-\-find\-adapters\-with\-sliding\-window\fR
+find adapters with simple
+sliding window algorithm
+.TP
+\fB\-\-no\-bgzf\-compression\fR
+turn off BGZF compression for
+FASTQ files
+.TP
+\fB\-\-fastq\-compression\-level\fR arg (=4)
+zlib compression level (1\-9)
+used for FASTQ files
+.TP
+\fB\-\-barcode\-mismatches\fR arg (=1)
+number of allowed mismatches
+per index
+Multiple, comma delimited,
+entries allowed. Each entry
+is applied to the
+corresponding index; last
+entry applies to all
+remaining indices.
+Accepted values: 0, 1, 2.
+.TP
+\fB\-\-no\-lane\-splitting\fR
+do not split fastq files by
+lane.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.


=====================================
debian/createmanpages
=====================================
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,22 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=bcl2fastq
+help2man --no-info --no-discard-stderr  \
+         --name='BCL to FASTQ file converter' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+



View it on GitLab: https://salsa.debian.org/med-team/bcl2fastq2/commit/4c9e9ee4aab91271fc33db0a502fb1cb7c55c84d

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View it on GitLab: https://salsa.debian.org/med-team/bcl2fastq2/commit/4c9e9ee4aab91271fc33db0a502fb1cb7c55c84d
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