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Build branch main with version main (ec69d9a)

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Build pipeline: viash-hub.biobox.main-t2txs

Source commit: ec69d9af7a

Source message: FEAT: update busco to 5.7.1 (#72)

* FEAT: update busco to 5.7.1

* Typo
This commit is contained in:
CI
2024-07-01 20:19:17 +00:00
parent bece67ad47
commit ae3fef8eec
125 changed files with 2030 additions and 268 deletions
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22
target/executable/cutadapt/.config.vsh.yaml
View File

@@ -305,6 +305,26 @@ argument_groups:
\ If match is on reverse-complemented version,\noutput that one.\n"
info: null
direction: "input"
- name: "Demultiplexing options"
arguments:
- type: "string"
name: "--demultiplex_mode"
description: "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual',\
\ adapters from the first and second read are used,\nand the indexes from the\
\ reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode\
\ 'combinatorial_dual' allows all combinations of the sets of indexes\non R1\
\ and R2. It is necessary to write each read pair to an output\nfile depending\
\ on the adapters found on both R1 and R2.\nMode 'single', uses indexes or barcodes\
\ located at the 5'\nend of the R1 read (single). \n"
info: null
required: false
choices:
- "single"
- "unique_dual"
- "combinatorial_dual"
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Read modifications"
arguments:
- type: "integer"
@@ -707,7 +727,7 @@ build_info:
output: "target/executable/cutadapt"
executable: "target/executable/cutadapt/cutadapt"
viash_version: "0.9.0-RC6"
git_commit: "3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
git_commit: "ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

75
target/executable/cutadapt/cutadapt
View File

@@ -357,6 +357,22 @@ function ViashHelp {
echo " matches. If match is on reverse-complemented version,"
echo " output that one."
echo ""
echo "Demultiplexing options:"
echo " --demultiplex_mode"
echo " type: string"
echo " choices: [ single, unique_dual, combinatorial_dual ]"
echo " Enable demultiplexing and set the mode for it."
echo " With mode 'unique_dual', adapters from the first and second read are"
echo " used,"
echo " and the indexes from the reads are only used in pairs. This implies"
echo " --pair_adapters."
echo " Enabling mode 'combinatorial_dual' allows all combinations of the sets"
echo " of indexes"
echo " on R1 and R2. It is necessary to write each read pair to an output"
echo " file depending on the adapters found on both R1 and R2."
echo " Mode 'single', uses indexes or barcodes located at the 5'"
echo " end of the R1 read (single)."
echo ""
echo "Read modifications:"
echo " -u, --cut"
echo " type: integer, multiple values allowed"
@@ -810,9 +826,9 @@ RUN pip install --upgrade pip && \
RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
LABEL org.opencontainers.image.created="2024-07-01T10:12:46Z"
LABEL org.opencontainers.image.created="2024-07-01T20:00:27Z"
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
LABEL org.opencontainers.image.revision="3e08b5983fe0fd7d9c3b222044363e760bf6dd4a"
LABEL org.opencontainers.image.revision="ec69d9af7a59c2618a49bef7d0bf9afc743ca065"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1303,6 +1319,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_REVCOMP=true
shift 1
;;
--demultiplex_mode)
[ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEMULTIPLEX_MODE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --demultiplex_mode. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--demultiplex_mode=*)
[ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode=*\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEMULTIPLEX_MODE=$(ViashRemoveFlags "$1")
shift 1
;;
--cut)
if [ -z "$VIASH_PAR_CUT" ]; then
VIASH_PAR_CUT="$2"
@@ -2202,6 +2229,18 @@ if [ ! -z "$VIASH_PAR_ACTION" ]; then
unset IFS
fi
if [ ! -z "$VIASH_PAR_DEMULTIPLEX_MODE" ]; then
VIASH_PAR_DEMULTIPLEX_MODE_CHOICES=("single;unique_dual;combinatorial_dual")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_DEMULTIPLEX_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_DEMULTIPLEX_MODE;" ]]; then
ViashError '--demultiplex_mode' specified value of \'$VIASH_PAR_DEMULTIPLEX_MODE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
exit 1
fi
set +f
unset IFS
fi
if [ ! -z "$VIASH_PAR_REPORT" ]; then
VIASH_PAR_REPORT_CHOICES=("full;minimal")
IFS=';'
@@ -2378,6 +2417,7 @@ $( if [ ! -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then echo "${VIASH_PAR_MATCH
$( if [ ! -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then echo "${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_match_adapter_wildcards='&'#" ; else echo "# par_no_match_adapter_wildcards="; fi )
$( if [ ! -z ${VIASH_PAR_ACTION+x} ]; then echo "${VIASH_PAR_ACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_action='&'#" ; else echo "# par_action="; fi )
$( if [ ! -z ${VIASH_PAR_REVCOMP+x} ]; then echo "${VIASH_PAR_REVCOMP}" | sed "s#'#'\"'\"'#g;s#.*#par_revcomp='&'#" ; else echo "# par_revcomp="; fi )
$( if [ ! -z ${VIASH_PAR_DEMULTIPLEX_MODE+x} ]; then echo "${VIASH_PAR_DEMULTIPLEX_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_demultiplex_mode='&'#" ; else echo "# par_demultiplex_mode="; fi )
$( if [ ! -z ${VIASH_PAR_CUT+x} ]; then echo "${VIASH_PAR_CUT}" | sed "s#'#'\"'\"'#g;s#.*#par_cut='&'#" ; else echo "# par_cut="; fi )
$( if [ ! -z ${VIASH_PAR_CUT_R2+x} ]; then echo "${VIASH_PAR_CUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_cut_r2='&'#" ; else echo "# par_cut_r2="; fi )
$( if [ ! -z ${VIASH_PAR_NEXTSEQ_TRIM+x} ]; then echo "${VIASH_PAR_NEXTSEQ_TRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_nextseq_trim='&'#" ; else echo "# par_nextseq_trim="; fi )
@@ -2545,7 +2585,7 @@ mod_args=\$(echo \\
\${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\
\${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\
\${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\
\${par_quality_cutoff_r2:+--quality-cutoff_r2 "\${par_quality_cutoff_r2}"} \\
\${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\
\${par_quality_base:+--quality-base "\${par_quality_base}"} \\
\${par_poly_a:+--poly-a} \\
\${par_length:+--length "\${par_length}"} \\
@@ -2614,14 +2654,35 @@ else
ext="fasta"
fi
if [ \$mode = "se" ]; then
demultiplex_mode="\$par_demultiplex_mode"
if [[ \$mode == "se" ]]; then
if [[ "\$demultiplex_mode" == "unique_dual" ]] || [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
echo "Demultiplexing dual indexes is not possible with single-end data."
exit 1
fi
prefix="trimmed_"
if [[ ! -z "\$demultiplex_mode" ]]; then
prefix="{name}_"
fi
output_args=\$(echo \\
--output "\$output_dir/{name}_001.\$ext" \\
--output "\$output_dir/\${prefix}001.\$ext" \\
)
else
demultiplex_indicator_r1='{name}_'
demultiplex_indicator_r2=\$demultiplex_indicator_r1
if [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
demultiplex_indicator_r1='{name1}_{name2}_'
demultiplex_indicator_r2='{name1}_{name2}_'
fi
prefix_r1="trimmed_"
prefix_r2="trimmed_"
if [[ ! -z "\$demultiplex_mode" ]]; then
prefix_r1=\$demultiplex_indicator_r1
prefix_r2=\$demultiplex_indicator_r2
fi
output_args=\$(echo \\
--output "\$output_dir/{name}_R1_001.\$ext" \\
--paired-output "\$output_dir/{name}_R2_001.\$ext" \\
--output "\$output_dir/\${prefix_r1}R1_001.\$ext" \\
--paired-output "\$output_dir/\${prefix_r2}R2_001.\$ext" \\
)
fi