Loading debian/bcl2fastq.1 0 → 100644 +172 −0 Original line number Diff line number Diff line .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 0 → 100755 +22 −0 Original line number Diff line number Diff line #!/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 Loading
debian/bcl2fastq.1 0 → 100644 +172 −0 Original line number Diff line number Diff line .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 0 → 100755 +22 −0 Original line number Diff line number Diff line #!/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
