Commit a4ae8437 authored by Gerald Salin's avatar Gerald Salin
Browse files

added -Xmx2g option by default to avoid in fastq2sam congif files

corrected input file in gzip config file (mids becomes index)
parent b424e03a
......@@ -22,17 +22,17 @@ $;PLATFORM$;=null
$;SORT_ORDER$;=coordinate
;;
;; java options, example: -Xmx2g
$;JAVA_OPTIONS$; =
$;JAVA_OPTIONS$; = -Xmx2g
;;other options: see help page of fastq2bam
$;OTHER_OPTIONS$;=
[input]
;; Input file, first-end fastq to convert
$;INPUT_FILE$;=
$;INPUT_FILE$;=
;; The input list of first-end fastq to convert
$;INPUT_FILE_LIST$;= $;REPOSITORY_ROOT$;/output_repository/create_list_file/$;PIPELINEID$;_fastq1/filelist.list
;; Directory containing first-end fastq to convert
$;INPUT_DIRECTORY$; =
$;INPUT_DIRECTORY$; =
;; the following is only used when iterating over an INPUT_DIRECTORY
$;INPUT_EXTENSION$; = fastq
;; The input list of second-end fastq, mandatory even if empty
......@@ -63,10 +63,10 @@ $;GROUP_COUNT$; = 150
$;NODISTRIB$; = 0
;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
[include]
$;PROJECT_CONFIG$;=
......@@ -22,17 +22,17 @@ $;PLATFORM$;=null
$;SORT_ORDER$;=coordinate
;;
;; java options, example: -Xmx2g
$;JAVA_OPTIONS$; =
$;JAVA_OPTIONS$; = -Xmx2g
;;other options: see help page of fastq2bam
$;OTHER_OPTIONS$;=
[input]
;; Input file, first-end fastq to convert
$;INPUT_FILE$;=
$;INPUT_FILE$;=
;; The input list of first-end fastq to convert
$;INPUT_FILE_LIST$;= $;REPOSITORY_ROOT$;/output_repository/create_list_file/$;PIPELINEID$;_fastq1/filelist.list
;; Directory containing first-end fastq to convert
$;INPUT_DIRECTORY$; =
$;INPUT_DIRECTORY$; =
;; the following is only used when iterating over an INPUT_DIRECTORY
$;INPUT_EXTENSION$; = fastq
;; The input list of second-end fastq, mandatory even if empty
......@@ -63,10 +63,10 @@ $;GROUP_COUNT$; = 150
$;NODISTRIB$; = 0
;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
[include]
$;PROJECT_CONFIG$;=
......@@ -22,17 +22,17 @@ $;PLATFORM$;=null
$;SORT_ORDER$;=coordinate
;;
;; java options, example: -Xmx2g
$;JAVA_OPTIONS$; =
$;JAVA_OPTIONS$; = -Xmx2g
;;other options: see help page of fastq2bam
$;OTHER_OPTIONS$;=
[input]
;; Input file, first-end fastq to convert
$;INPUT_FILE$;=
$;INPUT_FILE$;=
;; The input list of first-end fastq to convert
$;INPUT_FILE_LIST$;= $;REPOSITORY_ROOT$;/output_repository/create_list_file/$;PIPELINEID$;_fastq1/filelist.list
;; Directory containing first-end fastq to convert
$;INPUT_DIRECTORY$; =
$;INPUT_DIRECTORY$; =
;; the following is only used when iterating over an INPUT_DIRECTORY
$;INPUT_EXTENSION$; = fastq
;; The input list of second-end fastq, mandatory even if empty
......@@ -63,10 +63,10 @@ $;GROUP_COUNT$; = 150
$;NODISTRIB$; = 0
;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
$;COMPONENT_CONFIG$; =
$;COMPONENT_XML$; =
$;PIPELINE_XML$; =
$;PIPELINEID$; =
[include]
$;PROJECT_CONFIG$;=
......@@ -5,7 +5,7 @@ classification = general
[input]
$;INPUT_FILE_LIST$;=
$;INPUT_FILE$;=$;REPOSITORY_ROOT$;/output_repository/tarfiles/$;PIPELINEID$;_all_mids/`cat $;REPOSITORY_ROOT$;/output_repository/config_run/$;PIPELINEID$;_raw_input/prefix`all_mids_data.tar
$;INPUT_FILE$;=$;REPOSITORY_ROOT$;/output_repository/tarfiles/$;PIPELINEID$;_all_mids/`cat $;REPOSITORY_ROOT$;/output_repository/config_run/$;PIPELINEID$;_raw_input/prefix`all_index_data.tar
$;INPUT_DIRECTORY$;=
;; the following is only used when iterating over an INPUT_DIRECTORY
$;INPUT_EXTENSION$;=*
......
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