Build branch main with version main (8f525f5)
Build pipeline: viash-hub.biobox.main-x27rr
Source commit: 8f525f5e40
Source message: Bedtools_Intersect (#94)
* Initial Commit
* Update config.vsh.yaml
* creating templates
* Update config.vsh.yaml
* Update script.sh
* Added output
* Update config.vsh.yaml
* Update test.sh
* Update test.sh
* More tests
* small changes
* update
- change some var names
- debugged
- added more test
* Update CHANGELOG.md
* Update
* Update help.txt
This commit is contained in:
@@ -21,6 +21,9 @@
|
||||
|
||||
* `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
|
||||
|
||||
* `bedtools`:
|
||||
- `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
|
||||
|
||||
## MINOR CHANGES
|
||||
|
||||
* `busco` components: update BUSCO to `5.7.1` (PR #72).
|
||||
|
||||
255
src/bedtools/bedtools_intersect/config.vsh.yaml
Normal file
255
src/bedtools/bedtools_intersect/config.vsh.yaml
Normal file
@@ -0,0 +1,255 @@
|
||||
name: bedtools_intersect
|
||||
namespace: bedtools
|
||||
description: |
|
||||
bedtools intersect allows one to screen for overlaps between two sets of genomic features.
|
||||
Moreover, it allows one to have fine control as to how the intersections are reported.
|
||||
bedtools intersect works with both BED/GFF/VCF and BAM files as input.
|
||||
keywords: [feature intersection, BAM, BED, GFF, VCF]
|
||||
links:
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
repository: https://github.com/arq5x/bedtools2
|
||||
references:
|
||||
doi: 10.1093/bioinformatics/btq033
|
||||
license: GPL-2.0, MIT
|
||||
requirements:
|
||||
commands: [bedtools]
|
||||
authors:
|
||||
- __merge__: /src/_authors/theodoro_gasperin.yaml
|
||||
roles: [ author, maintainer ]
|
||||
|
||||
argument_groups:
|
||||
- name: Inputs
|
||||
arguments:
|
||||
- name: --input_a
|
||||
alternatives: -a
|
||||
type: file
|
||||
direction: input
|
||||
description: |
|
||||
The input file (BED/GFF/VCF/BAM) to be used as the -a file.
|
||||
required: true
|
||||
example: input_a.bed
|
||||
|
||||
- name: --input_b
|
||||
alternatives: -b
|
||||
type: file
|
||||
direction: input
|
||||
multiple: true
|
||||
description: |
|
||||
The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).
|
||||
required: true
|
||||
example: input_b.bed
|
||||
|
||||
- name: Outputs
|
||||
arguments:
|
||||
- name: --output
|
||||
type: file
|
||||
direction: output
|
||||
description: |
|
||||
The output BED file.
|
||||
required: true
|
||||
example: output.bed
|
||||
|
||||
- name: Options
|
||||
arguments:
|
||||
- name: --write_a
|
||||
alternatives: -wa
|
||||
type: boolean_true
|
||||
description: Write the original A entry for each overlap.
|
||||
|
||||
- name: --write_b
|
||||
alternatives: -wb
|
||||
type: boolean_true
|
||||
description: |
|
||||
Write the original B entry for each overlap.
|
||||
Useful for knowing _what_ A overlaps. Restricted by -f and -r.
|
||||
|
||||
- name: --left_outer_join
|
||||
alternatives: -loj
|
||||
type: boolean_true
|
||||
description: |
|
||||
Perform a "left outer join". That is, for each feature in A report each overlap with B.
|
||||
If no overlaps are found, report a NULL feature for B.
|
||||
|
||||
- name: --write_overlap
|
||||
alternatives: -wo
|
||||
type: boolean_true
|
||||
description: |
|
||||
Write the original A and B entries plus the number of base pairs of overlap between the two features.
|
||||
- Overlaps restricted by -f and -r.
|
||||
Only A features with overlap are reported.
|
||||
|
||||
- name: --write_overlap_plus
|
||||
alternatives: -wao
|
||||
type: boolean_true
|
||||
description: |
|
||||
Write the original A and B entries plus the number of base pairs of overlap between the two features.
|
||||
- Overlaps restricted by -f and -r.
|
||||
However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.
|
||||
|
||||
- name: --report_A_if_no_overlap
|
||||
alternatives: -u
|
||||
type: boolean_true
|
||||
description: |
|
||||
Write the original A entry _if_ no overlap is found.
|
||||
- In other words, just report the fact >=1 hit was found.
|
||||
- Overlaps restricted by -f and -r.
|
||||
|
||||
- name: --number_of_overlaps_A
|
||||
alternatives: -c
|
||||
type: boolean_true
|
||||
description: |
|
||||
For each entry in A, report the number of overlaps with B.
|
||||
- Reports 0 for A entries that have no overlap with B.
|
||||
- Overlaps restricted by -f and -r.
|
||||
|
||||
- name: --report_no_overlaps_A
|
||||
alternatives: -v
|
||||
type: boolean_true
|
||||
description: |
|
||||
Only report those entries in A that have _no overlaps_ with B.
|
||||
- Similar to "grep -v" (an homage).
|
||||
|
||||
- name: --uncompressed_bam
|
||||
alternatives: -ubam
|
||||
type: boolean_true
|
||||
description: Write uncompressed BAM output. Default writes compressed BAM.
|
||||
|
||||
- name: --same_strand
|
||||
alternatives: -s
|
||||
type: boolean_true
|
||||
description: |
|
||||
Require same strandedness. That is, only report hits in B.
|
||||
that overlap A on the _same_ strand.
|
||||
- By default, overlaps are reported without respect to strand.
|
||||
|
||||
- name: --opposite_strand
|
||||
alternatives: -S
|
||||
type: boolean_true
|
||||
description: |
|
||||
Require different strandedness. That is, only report hits in B
|
||||
that overlap A on the _opposite_ strand.
|
||||
- By default, overlaps are reported without respect to strand.
|
||||
|
||||
- name: --min_overlap_A
|
||||
alternatives: -f
|
||||
type: double
|
||||
description: |
|
||||
Minimum overlap required as a fraction of A.
|
||||
- Default is 1E-9 (i.e., 1bp).
|
||||
- FLOAT (e.g. 0.50)
|
||||
example: 0.50
|
||||
|
||||
- name: --min_overlap_B
|
||||
alternatives: -F
|
||||
type: double
|
||||
description: |
|
||||
Minimum overlap required as a fraction of B.
|
||||
- Default is 1E-9 (i.e., 1bp).
|
||||
- FLOAT (e.g. 0.50)
|
||||
example: 0.50
|
||||
|
||||
- name: --reciprocal_overlap
|
||||
alternatives: -r
|
||||
type: boolean_true
|
||||
description: |
|
||||
Require that the fraction overlap be reciprocal for A AND B.
|
||||
- In other words, if -f is 0.90 and -r is used, this requires
|
||||
that B overlap 90% of A and A _also_ overlaps 90% of B.
|
||||
|
||||
- name: --either_overlap
|
||||
alternatives: -e
|
||||
type: boolean_true
|
||||
description: |
|
||||
Require that the minimum fraction be satisfied for A OR B.
|
||||
- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
|
||||
that either 90% of A is covered OR 10% of B is covered.
|
||||
Without -e, both fractions would have to be satisfied.
|
||||
|
||||
- name: --split
|
||||
type: boolean_true
|
||||
description: Treat "split" BAM or BED12 entries as distinct BED intervals.
|
||||
|
||||
- name: --genome
|
||||
alternatives: -g
|
||||
type: file
|
||||
description: |
|
||||
Provide a genome file to enforce consistent chromosome
|
||||
sort order across input files. Only applies when used
|
||||
with -sorted option.
|
||||
example: genome.txt
|
||||
|
||||
- name: --nonamecheck
|
||||
type: boolean_true
|
||||
description: |
|
||||
For sorted data, don't throw an error if the file
|
||||
has different naming conventions for the same chromosome
|
||||
(e.g., "chr1" vs "chr01").
|
||||
|
||||
- name: --sorted
|
||||
type: boolean_true
|
||||
description: |
|
||||
Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
|
||||
|
||||
- name: --names
|
||||
type: string
|
||||
description: |
|
||||
When using multiple databases, provide an alias
|
||||
for each that will appear instead of a fileId when
|
||||
also printing the DB record.
|
||||
|
||||
- name: --filenames
|
||||
type: boolean_true
|
||||
description: When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.
|
||||
|
||||
- name: --sortout
|
||||
type: boolean_true
|
||||
description: When using multiple databases, sort the output DB hits for each record.
|
||||
|
||||
- name: --bed
|
||||
type: boolean_true
|
||||
description: If using BAM input, write output as BED.
|
||||
|
||||
- name: --header
|
||||
type: boolean_true
|
||||
description: Print the header from the A file prior to results.
|
||||
|
||||
- name: --no_buffer_output
|
||||
alternatives: --nobuf
|
||||
type: boolean_true
|
||||
description: |
|
||||
Disable buffered output. Using this option will cause each line
|
||||
of output to be printed as it is generated, rather than saved
|
||||
in a buffer. This will make printing large output files
|
||||
noticeably slower, but can be useful in conjunction with
|
||||
other software tools and scripts that need to process one
|
||||
line of bedtools output at a time.
|
||||
|
||||
- name: --io_buffer_size
|
||||
alternatives: --iobuf
|
||||
type: integer
|
||||
description: |
|
||||
Specify amount of memory to use for input buffer.
|
||||
Takes an integer argument. Optional suffixes K/M/G supported.
|
||||
Note: currently has no effect with compressed files.
|
||||
|
||||
resources:
|
||||
- type: bash_script
|
||||
path: script.sh
|
||||
|
||||
test_resources:
|
||||
- type: bash_script
|
||||
path: test.sh
|
||||
|
||||
engines:
|
||||
- type: docker
|
||||
image: debian:stable-slim
|
||||
setup:
|
||||
- type: apt
|
||||
packages: [bedtools, procps]
|
||||
- type: docker
|
||||
run: |
|
||||
echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
|
||||
|
||||
runners:
|
||||
- type: executable
|
||||
- type: nextflow
|
||||
119
src/bedtools/bedtools_intersect/help.txt
Normal file
119
src/bedtools/bedtools_intersect/help.txt
Normal file
@@ -0,0 +1,119 @@
|
||||
```bash
|
||||
bedtools intersect
|
||||
```
|
||||
|
||||
Tool: bedtools intersect (aka intersectBed)
|
||||
Version: v2.30.0
|
||||
Summary: Report overlaps between two feature files.
|
||||
|
||||
Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
|
||||
|
||||
Note: -b may be followed with multiple databases and/or
|
||||
wildcard (*) character(s).
|
||||
Options:
|
||||
-wa Write the original entry in A for each overlap.
|
||||
|
||||
-wb Write the original entry in B for each overlap.
|
||||
- Useful for knowing _what_ A overlaps. Restricted by -f and -r.
|
||||
|
||||
-loj Perform a "left outer join". That is, for each feature in A
|
||||
report each overlap with B. If no overlaps are found,
|
||||
report a NULL feature for B.
|
||||
|
||||
-wo Write the original A and B entries plus the number of base
|
||||
pairs of overlap between the two features.
|
||||
- Overlaps restricted by -f and -r.
|
||||
Only A features with overlap are reported.
|
||||
|
||||
-wao Write the original A and B entries plus the number of base
|
||||
pairs of overlap between the two features.
|
||||
- Overlapping features restricted by -f and -r.
|
||||
However, A features w/o overlap are also reported
|
||||
with a NULL B feature and overlap = 0.
|
||||
|
||||
-u Write the original A entry _once_ if _any_ overlaps found in B.
|
||||
- In other words, just report the fact >=1 hit was found.
|
||||
- Overlaps restricted by -f and -r.
|
||||
|
||||
-c For each entry in A, report the number of overlaps with B.
|
||||
- Reports 0 for A entries that have no overlap with B.
|
||||
- Overlaps restricted by -f, -F, -r, and -s.
|
||||
|
||||
-C For each entry in A, separately report the number of
|
||||
- overlaps with each B file on a distinct line.
|
||||
- Reports 0 for A entries that have no overlap with B.
|
||||
- Overlaps restricted by -f, -F, -r, and -s.
|
||||
|
||||
-v Only report those entries in A that have _no overlaps_ with B.
|
||||
- Similar to "grep -v" (an homage).
|
||||
|
||||
-ubam Write uncompressed BAM output. Default writes compressed BAM.
|
||||
|
||||
-s Require same strandedness. That is, only report hits in B
|
||||
that overlap A on the _same_ strand.
|
||||
- By default, overlaps are reported without respect to strand.
|
||||
|
||||
-S Require different strandedness. That is, only report hits in B
|
||||
that overlap A on the _opposite_ strand.
|
||||
- By default, overlaps are reported without respect to strand.
|
||||
|
||||
-f Minimum overlap required as a fraction of A.
|
||||
- Default is 1E-9 (i.e., 1bp).
|
||||
- FLOAT (e.g. 0.50)
|
||||
|
||||
-F Minimum overlap required as a fraction of B.
|
||||
- Default is 1E-9 (i.e., 1bp).
|
||||
- FLOAT (e.g. 0.50)
|
||||
|
||||
-r Require that the fraction overlap be reciprocal for A AND B.
|
||||
- In other words, if -f is 0.90 and -r is used, this requires
|
||||
that B overlap 90% of A and A _also_ overlaps 90% of B.
|
||||
|
||||
-e Require that the minimum fraction be satisfied for A OR B.
|
||||
- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
|
||||
that either 90% of A is covered OR 10% of B is covered.
|
||||
Without -e, both fractions would have to be satisfied.
|
||||
|
||||
-split Treat "split" BAM or BED12 entries as distinct BED intervals.
|
||||
|
||||
-g Provide a genome file to enforce consistent chromosome sort order
|
||||
across input files. Only applies when used with -sorted option.
|
||||
|
||||
-nonamecheck For sorted data, don't throw an error if the file has different naming conventions
|
||||
for the same chromosome. ex. "chr1" vs "chr01".
|
||||
|
||||
-sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
|
||||
|
||||
-names When using multiple databases, provide an alias for each that
|
||||
will appear instead of a fileId when also printing the DB record.
|
||||
|
||||
-filenames When using multiple databases, show each complete filename
|
||||
instead of a fileId when also printing the DB record.
|
||||
|
||||
-sortout When using multiple databases, sort the output DB hits
|
||||
for each record.
|
||||
|
||||
-bed If using BAM input, write output as BED.
|
||||
|
||||
-header Print the header from the A file prior to results.
|
||||
|
||||
-nobuf Disable buffered output. Using this option will cause each line
|
||||
of output to be printed as it is generated, rather than saved
|
||||
in a buffer. This will make printing large output files
|
||||
noticeably slower, but can be useful in conjunction with
|
||||
other software tools and scripts that need to process one
|
||||
line of bedtools output at a time.
|
||||
|
||||
-iobuf Specify amount of memory to use for input buffer.
|
||||
Takes an integer argument. Optional suffixes K/M/G supported.
|
||||
Note: currently has no effect with compressed files.
|
||||
|
||||
Notes:
|
||||
(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
|
||||
and excluded if an overlap cannot be found. If multiple overlaps exist, they are not
|
||||
reported, as we are only testing for one or more overlaps.
|
||||
|
||||
|
||||
|
||||
|
||||
***** ERROR: No input file given. Exiting. *****
|
||||
61
src/bedtools/bedtools_intersect/script.sh
Normal file
61
src/bedtools/bedtools_intersect/script.sh
Normal file
@@ -0,0 +1,61 @@
|
||||
#!/bin/bash
|
||||
|
||||
## VIASH START
|
||||
## VIASH END
|
||||
|
||||
[[ "$par_write_a" == "false" ]] && unset par_write_a
|
||||
[[ "$par_write_b" == "false" ]] && unset par_write_b
|
||||
[[ "$par_left_outer_join" == "false" ]] && unset par_left_outer_join
|
||||
[[ "$par_write_overlap" == "false" ]] && unset par_write_overlap
|
||||
[[ "$par_write_overlap_plus" == "false" ]] && unset par_write_overlap_plus
|
||||
[[ "$par_report_A_if_no_overlap" == "false" ]] && unset par_report_A_if_no_overlap
|
||||
[[ "$par_number_of_overlaps_A" == "false" ]] && unset par_number_of_overlaps_A
|
||||
[[ "$par_report_no_overlaps_A" == "false" ]] && unset par_report_no_overlaps_A
|
||||
[[ "$par_uncompressed_bam" == "false" ]] && unset par_uncompressed_bam
|
||||
[[ "$par_same_strand" == "false" ]] && unset par_same_strand
|
||||
[[ "$par_opposite_strand" == "false" ]] && unset par_opposite_strand
|
||||
[[ "$par_reciprocal_overlap" == "false" ]] && unset par_reciprocal_overlap
|
||||
[[ "$par_either_overlap" == "false" ]] && unset par_either_overlap
|
||||
[[ "$par_split" == "false" ]] && unset par_split
|
||||
[[ "$par_nonamecheck" == "false" ]] && unset par_nonamecheck
|
||||
[[ "$par_sorted" == "false" ]] && unset par_sorted
|
||||
[[ "$par_filenames" == "false" ]] && unset par_filenames
|
||||
[[ "$par_sortout" == "false" ]] && unset par_sortout
|
||||
[[ "$par_bed" == "false" ]] && unset par_bed
|
||||
[[ "$par_header" == "false" ]] && unset par_header
|
||||
[[ "$par_no_buffer_output" == "false" ]] && unset par_no_buffer_output
|
||||
|
||||
# Create input array
|
||||
IFS=";" read -ra input <<< $par_input_b
|
||||
|
||||
bedtools intersect \
|
||||
${par_write_a:+-wa} \
|
||||
${par_write_b:+-wb} \
|
||||
${par_left_outer_join:+-loj} \
|
||||
${par_write_overlap:+-wo} \
|
||||
${par_write_overlap_plus:+-wao} \
|
||||
${par_report_A_if_no_overlap:+-u} \
|
||||
${par_number_of_overlaps_A:+-c} \
|
||||
${par_report_no_overlaps_A:+-v} \
|
||||
${par_uncompressed_bam:+-ubam} \
|
||||
${par_same_strand:+-s} \
|
||||
${par_opposite_strand:+-S} \
|
||||
${par_min_overlap_A:+-f "$par_min_overlap_A"} \
|
||||
${par_min_overlap_B:+-F "$par_min_overlap_B"} \
|
||||
${par_reciprocal_overlap:+-r} \
|
||||
${par_either_overlap:+-e} \
|
||||
${par_split:+-split} \
|
||||
${par_genome:+-g "$par_genome"} \
|
||||
${par_nonamecheck:+-nonamecheck} \
|
||||
${par_sorted:+-sorted} \
|
||||
${par_names:+-names "$par_names"} \
|
||||
${par_filenames:+-filenames} \
|
||||
${par_sortout:+-sortout} \
|
||||
${par_bed:+-bed} \
|
||||
${par_header:+-header} \
|
||||
${par_no_buffer_output:+-nobuf} \
|
||||
${par_io_buffer_size:+-iobuf "$par_io_buffer_size"} \
|
||||
-a "$par_input_a" \
|
||||
${par_input_b:+ -b ${input[*]}} \
|
||||
> "$par_output"
|
||||
|
||||
340
src/bedtools/bedtools_intersect/test.sh
Normal file
340
src/bedtools/bedtools_intersect/test.sh
Normal file
@@ -0,0 +1,340 @@
|
||||
#!/bin/bash
|
||||
|
||||
# exit on error
|
||||
set -e
|
||||
|
||||
## VIASH START
|
||||
meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect"
|
||||
meta_resources_dir="src/bedtools/bedtools_intersect"
|
||||
## VIASH END
|
||||
|
||||
#############################################
|
||||
# helper functions
|
||||
assert_file_exists() {
|
||||
[ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
|
||||
}
|
||||
assert_file_not_empty() {
|
||||
[ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
|
||||
}
|
||||
assert_file_contains() {
|
||||
grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
|
||||
}
|
||||
assert_identical_content() {
|
||||
diff -a "$2" "$1" \
|
||||
|| (echo "Files are not identical!" && exit 1)
|
||||
}
|
||||
#############################################
|
||||
|
||||
# Create directories for tests
|
||||
echo "Creating Test Data..."
|
||||
mkdir -p test_data
|
||||
|
||||
# Create and populate featuresA.bed
|
||||
printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/featuresA.bed"
|
||||
|
||||
# Create and populate featuresB.bed
|
||||
printf "chr1\t180\t280\nchr1\t290\t390\nchr1\t500\t600\n" > "test_data/featuresB.bed"
|
||||
|
||||
# Create and populate featuresC.bed
|
||||
printf "chr1\t120\t220\nchr1\t250\t350\nchr1\t500\t580\n" > "test_data/featuresC.bed"
|
||||
|
||||
# Create and populate examples gff files
|
||||
# example1.gff
|
||||
printf "##gff-version 3\n" > "test_data/example1.gff"
|
||||
printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example1.gff"
|
||||
printf "chr1\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example1.gff"
|
||||
printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example1.gff"
|
||||
printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example1.gff"
|
||||
printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example1.gff"
|
||||
printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example1.gff"
|
||||
# example2.gff
|
||||
printf "##gff-version 3\n" > "test_data/example2.gff"
|
||||
printf "chr1\t.\tgene\t1200\t1800\t.\t-\t.\tID=gene2;Name=Gene2\n" >> "test_data/example2.gff"
|
||||
printf "chr1\t.\tmRNA\t1400\t2000\t.\t-\t.\tID=transcript2;Parent=gene2\n" >> "test_data/example2.gff"
|
||||
printf "chr1\t.\texon\t1400\t2000\t.\t-\t.\tID=exon3;Parent=transcript2\n" >> "test_data/example2.gff"
|
||||
printf "chr1\t.\texon\t1600\t2000\t.\t-\t.\tID=exon4;Parent=transcript2\n" >> "test_data/example2.gff"
|
||||
printf "chr1\t.\tCDS\t3000\t3200\t.\t-\t1\tID=cds3;Parent=transcript2\n" >> "test_data/example2.gff"
|
||||
printf "chr1\t.\tCDS\t3500\t3700\t.\t-\t0\tID=cds4;Parent=transcript2\n" >> "test_data/example2.gff"
|
||||
|
||||
# Create and populate expected output files for different tests
|
||||
printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_default.bed"
|
||||
printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_wa.bed"
|
||||
printf "chr1\t180\t200\tchr1\t180\t280\nchr1\t180\t250\tchr1\t180\t280\nchr1\t300\t390\tchr1\t290\t390\n" > "test_data/expected_wb.bed"
|
||||
printf "chr1\t100\t200\tchr1\t180\t280\nchr1\t150\t250\tchr1\t180\t280\nchr1\t300\t400\tchr1\t290\t390\n" > "test_data/expected_loj.bed"
|
||||
printf "chr1\t100\t200\tchr1\t180\t280\t20\nchr1\t150\t250\tchr1\t180\t280\t70\nchr1\t300\t400\tchr1\t290\t390\t90\n" > "test_data/expected_wo.bed"
|
||||
printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_u.bed"
|
||||
printf "chr1\t100\t200\t1\nchr1\t150\t250\t1\nchr1\t300\t400\t1\n" > "test_data/expected_c.bed"
|
||||
printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f50.bed"
|
||||
printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f30.bed"
|
||||
printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f10.bed"
|
||||
printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_r.bed"
|
||||
printf "chr1\t180\t200\nchr1\t120\t200\nchr1\t180\t250\nchr1\t150\t220\nchr1\t300\t390\nchr1\t300\t350\n" > "test_data/expected_multiple.bed"
|
||||
# expected gff file
|
||||
printf "chr1\t.\tgene\t1200\t1800\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tgene\t1600\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tmRNA\t1200\t1800\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tmRNA\t1600\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\texon\t1200\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\texon\t1600\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tCDS\t1200\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
printf "chr1\t.\tCDS\t1600\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
|
||||
|
||||
# Test 1: Default intersect
|
||||
mkdir test1
|
||||
cd test1
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with default intersect"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed"
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_default.bed"
|
||||
echo "- test1 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 2: Write A option
|
||||
mkdir test2
|
||||
cd test2
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -wa option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--write_a
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_wa.bed"
|
||||
echo "- test2 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 3: -wb option
|
||||
mkdir test3
|
||||
cd test3
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -wb option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--write_b
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_wb.bed"
|
||||
echo "- test3 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 4: -loj option
|
||||
mkdir test4
|
||||
cd test4
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -loj option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--left_outer_join
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_loj.bed"
|
||||
echo "- test4 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 5: -wo option
|
||||
mkdir test5
|
||||
cd test5
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -wo option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--write_overlap
|
||||
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_wo.bed"
|
||||
echo "- test5 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 6: -u option
|
||||
mkdir test6
|
||||
cd test6
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -u option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--report_A_if_no_overlap true
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_u.bed"
|
||||
echo "- test6 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 7: -c option
|
||||
mkdir test7
|
||||
cd test7
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -c option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--number_of_overlaps_A true
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_c.bed"
|
||||
echo "- test7 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 8: -f 0.50 option
|
||||
mkdir test8
|
||||
cd test8
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -f 0.50 option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--min_overlap_A 0.50
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_f50.bed"
|
||||
echo "- test8 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 9: -f 0.30 option
|
||||
mkdir test9
|
||||
cd test9
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -f 0.30 option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--min_overlap_A 0.30
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_f30.bed"
|
||||
echo "- test9 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 10: -f 0.10 option
|
||||
mkdir test10
|
||||
cd test10
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -f 0.10 option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--min_overlap_A 0.10
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_f10.bed"
|
||||
echo "- test10 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 11: -r option
|
||||
mkdir test11
|
||||
cd test11
|
||||
|
||||
echo "> Run bedtools_intersect on BED files with -r option"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--output "output.bed" \
|
||||
--reciprocal_overlap true
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_r.bed"
|
||||
echo "- test11 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
|
||||
# Test 12: Multiple files
|
||||
mkdir test12
|
||||
cd test12
|
||||
|
||||
echo "> Run bedtools_intersect on multiple BED files"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/featuresA.bed" \
|
||||
--input_b "../test_data/featuresB.bed" \
|
||||
--input_b "../test_data/featuresC.bed" \
|
||||
--output "output.bed"
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected_multiple.bed"
|
||||
echo "- test12 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
# Test 13: VCF file format
|
||||
mkdir test13
|
||||
cd test13
|
||||
|
||||
echo "> Run bedtools_intersect on GFF files"
|
||||
"$meta_executable" \
|
||||
--input_a "../test_data/example1.gff" \
|
||||
--input_b "../test_data/example2.gff" \
|
||||
--output "output.bed"
|
||||
|
||||
# checks
|
||||
assert_file_exists "output.bed"
|
||||
assert_file_not_empty "output.bed"
|
||||
assert_identical_content "output.bed" "../test_data/expected.gff"
|
||||
echo "- test13 succeeded -"
|
||||
|
||||
cd ..
|
||||
|
||||
echo "---- All tests succeeded! ----"
|
||||
exit 0
|
||||
@@ -228,7 +228,7 @@ build_info:
|
||||
output: "target/executable/agat/agat_convert_sp_gff2gtf"
|
||||
executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -518,9 +518,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
|
||||
|
||||
LABEL org.opencontainers.image.authors="Leïla Paquay"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:07Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -706,7 +706,7 @@ build_info:
|
||||
output: "target/executable/arriba"
|
||||
executable: "target/executable/arriba/arriba"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -753,9 +753,9 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' >
|
||||
|
||||
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component arriba"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:02Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:58Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -418,7 +418,7 @@ build_info:
|
||||
output: "target/executable/bcl_convert"
|
||||
executable: "target/executable/bcl_convert/bcl_convert"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -598,9 +598,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
|
||||
|
||||
LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:02Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:59Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -270,7 +270,7 @@ build_info:
|
||||
output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
|
||||
executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -548,9 +548,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:06Z"
|
||||
LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -232,7 +232,7 @@ build_info:
|
||||
output: "target/executable/bedtools/bedtools_getfasta"
|
||||
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -525,9 +525,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dries Schaumont"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:04Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:01Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
436
target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
Normal file
436
target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
Normal file
@@ -0,0 +1,436 @@
|
||||
name: "bedtools_intersect"
|
||||
namespace: "bedtools"
|
||||
version: "main"
|
||||
authors:
|
||||
- name: "Theodoro Gasperin Terra Camargo"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
links:
|
||||
email: "theodorogtc@gmail.com"
|
||||
github: "tgaspe"
|
||||
linkedin: "theodoro-gasperin-terra-camargo"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatician"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_a"
|
||||
alternatives:
|
||||
- "-a"
|
||||
description: "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
|
||||
info: null
|
||||
example:
|
||||
- "input_a.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input_b"
|
||||
alternatives:
|
||||
- "-b"
|
||||
description: "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
|
||||
info: null
|
||||
example:
|
||||
- "input_b.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "The output BED file. \n"
|
||||
info: null
|
||||
example:
|
||||
- "output.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Options"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--write_a"
|
||||
alternatives:
|
||||
- "-wa"
|
||||
description: "Write the original A entry for each overlap."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_b"
|
||||
alternatives:
|
||||
- "-wb"
|
||||
description: "Write the original B entry for each overlap. \nUseful for knowing\
|
||||
\ _what_ A overlaps. Restricted by -f and -r.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--left_outer_join"
|
||||
alternatives:
|
||||
- "-loj"
|
||||
description: "Perform a \"left outer join\". That is, for each feature in A report\
|
||||
\ each overlap with B. \nIf no overlaps are found, report a NULL feature for\
|
||||
\ B.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_overlap"
|
||||
alternatives:
|
||||
- "-wo"
|
||||
description: "Write the original A and B entries plus the number of base pairs\
|
||||
\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
|
||||
\ \n Only A features with overlap are reported.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_overlap_plus"
|
||||
alternatives:
|
||||
- "-wao"
|
||||
description: "Write the original A and B entries plus the number of base pairs\
|
||||
\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
|
||||
\ \n However, A features w/o overlap are also reported with a NULL B feature\
|
||||
\ and overlap = 0.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--report_A_if_no_overlap"
|
||||
alternatives:
|
||||
- "-u"
|
||||
description: "Write the original A entry _if_ no overlap is found. \n- In other\
|
||||
\ words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f\
|
||||
\ and -r. \n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--number_of_overlaps_A"
|
||||
alternatives:
|
||||
- "-c"
|
||||
description: "For each entry in A, report the number of overlaps with B.\n- Reports\
|
||||
\ 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f\
|
||||
\ and -r.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--report_no_overlaps_A"
|
||||
alternatives:
|
||||
- "-v"
|
||||
description: "Only report those entries in A that have _no overlaps_ with B.\n\
|
||||
- Similar to \"grep -v\" (an homage).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--uncompressed_bam"
|
||||
alternatives:
|
||||
- "-ubam"
|
||||
description: "Write uncompressed BAM output. Default writes compressed BAM."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--same_strand"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Require same strandedness. That is, only report hits in B.\nthat\
|
||||
\ overlap A on the _same_ strand.\n- By default, overlaps are reported without\
|
||||
\ respect to strand.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--opposite_strand"
|
||||
alternatives:
|
||||
- "-S"
|
||||
description: "Require different strandedness. That is, only report hits in B\n\
|
||||
that overlap A on the _opposite_ strand.\n- By default, overlaps are reported\
|
||||
\ without respect to strand.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "double"
|
||||
name: "--min_overlap_A"
|
||||
alternatives:
|
||||
- "-f"
|
||||
description: "Minimum overlap required as a fraction of A.\n- Default is 1E-9\
|
||||
\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
info: null
|
||||
example:
|
||||
- 0.5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--min_overlap_B"
|
||||
alternatives:
|
||||
- "-F"
|
||||
description: "Minimum overlap required as a fraction of B.\n- Default is 1E-9\
|
||||
\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
info: null
|
||||
example:
|
||||
- 0.5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--reciprocal_overlap"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "Require that the fraction overlap be reciprocal for A AND B.\n-\
|
||||
\ In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap\
|
||||
\ 90% of A and A _also_ overlaps 90% of B.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--either_overlap"
|
||||
alternatives:
|
||||
- "-e"
|
||||
description: "Require that the minimum fraction be satisfied for A OR B.\n- In\
|
||||
\ other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either\
|
||||
\ 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would\
|
||||
\ have to be satisfied.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--split"
|
||||
description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "file"
|
||||
name: "--genome"
|
||||
alternatives:
|
||||
- "-g"
|
||||
description: "Provide a genome file to enforce consistent chromosome \nsort order\
|
||||
\ across input files. Only applies when used \nwith -sorted option.\n"
|
||||
info: null
|
||||
example:
|
||||
- "genome.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--nonamecheck"
|
||||
description: "For sorted data, don't throw an error if the file \nhas different\
|
||||
\ naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\"\
|
||||
).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--sorted"
|
||||
description: "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--names"
|
||||
description: "When using multiple databases, provide an alias \nfor each that\
|
||||
\ will appear instead of a fileId when \nalso printing the DB record.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--filenames"
|
||||
description: "When using multiple databases, show each complete filename instead\
|
||||
\ of a fileId when also printing the DB record."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--sortout"
|
||||
description: "When using multiple databases, sort the output DB hits for each\
|
||||
\ record."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--bed"
|
||||
description: "If using BAM input, write output as BED."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--header"
|
||||
description: "Print the header from the A file prior to results."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--no_buffer_output"
|
||||
alternatives:
|
||||
- "--nobuf"
|
||||
description: "Disable buffered output. Using this option will cause each line\n\
|
||||
of output to be printed as it is generated, rather than saved\nin a buffer.\
|
||||
\ This will make printing large output files \nnoticeably slower, but can be\
|
||||
\ useful in conjunction with\nother software tools and scripts that need to\
|
||||
\ process one\nline of bedtools output at a time.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--io_buffer_size"
|
||||
alternatives:
|
||||
- "--iobuf"
|
||||
description: "Specify amount of memory to use for input buffer.\nTakes an integer\
|
||||
\ argument. Optional suffixes K/M/G supported.\nNote: currently has no effect\
|
||||
\ with compressed files. \n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "bedtools intersect allows one to screen for overlaps between two sets\
|
||||
\ of genomic features. \nMoreover, it allows one to have fine control as to how\
|
||||
\ the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF\
|
||||
\ and BAM files as input.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "feature intersection"
|
||||
- "BAM"
|
||||
- "BED"
|
||||
- "GFF"
|
||||
- "VCF"
|
||||
license: "GPL-2.0, MIT"
|
||||
references:
|
||||
doi:
|
||||
- "10.1093/bioinformatics/btq033"
|
||||
links:
|
||||
repository: "https://github.com/arq5x/bedtools2"
|
||||
documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "bedtools"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
|
||||
\ > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/bedtools/bedtools_intersect/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/bedtools/bedtools_intersect"
|
||||
executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
version: "main"
|
||||
description: "A collection of bioinformatics tools for working with sequence data.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "modules"
|
||||
- "sequencing"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/biobox"
|
||||
issue_tracker: "https://github.com/viash-hub/biobox/issues"
|
||||
1842
target/executable/bedtools/bedtools_intersect/bedtools_intersect
Executable file
1842
target/executable/bedtools/bedtools_intersect/bedtools_intersect
Executable file
File diff suppressed because it is too large
Load Diff
@@ -158,7 +158,7 @@ build_info:
|
||||
output: "target/executable/busco/busco_download_datasets"
|
||||
executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -474,9 +474,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:00Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
|
||||
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -145,7 +145,7 @@ build_info:
|
||||
output: "target/executable/busco/busco_list_datasets"
|
||||
executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -464,9 +464,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:00Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
|
||||
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -423,7 +423,7 @@ build_info:
|
||||
output: "target/executable/busco/busco_run"
|
||||
executable: "target/executable/busco/busco_run/busco_run"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -631,9 +631,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:01Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:57Z"
|
||||
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -740,7 +740,7 @@ build_info:
|
||||
output: "target/executable/cutadapt"
|
||||
executable: "target/executable/cutadapt/cutadapt"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -830,9 +830,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions
|
||||
|
||||
LABEL org.opencontainers.image.authors="Toni Verbeiren"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:57:59Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:55Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -317,7 +317,7 @@ build_info:
|
||||
output: "target/executable/falco"
|
||||
executable: "target/executable/falco/falco"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -588,9 +588,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio
|
||||
|
||||
LABEL org.opencontainers.image.authors="Toni Verbeiren"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component falco"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:57:59Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:56Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1083,7 +1083,7 @@ build_info:
|
||||
output: "target/executable/fastp"
|
||||
executable: "target/executable/fastp/fastp"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -1027,9 +1027,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component fastp"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:04Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:01Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -645,7 +645,7 @@ build_info:
|
||||
output: "target/executable/featurecounts"
|
||||
executable: "target/executable/featurecounts/featurecounts"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -753,9 +753,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/
|
||||
|
||||
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:01Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:58Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -685,7 +685,7 @@ build_info:
|
||||
output: "target/executable/gffread"
|
||||
executable: "target/executable/gffread/gffread"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -806,9 +806,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gffread"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:00Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:56Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -507,7 +507,7 @@ build_info:
|
||||
output: "target/executable/lofreq/lofreq_call"
|
||||
executable: "target/executable/lofreq/lofreq_call/lofreq_call"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -655,9 +655,9 @@ echo "lofreq: $version" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Kai Waldrant"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:07Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -215,7 +215,7 @@ build_info:
|
||||
output: "target/executable/lofreq/lofreq_indelqual"
|
||||
executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -500,9 +500,9 @@ echo "lofreq: $version" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Kai Waldrant"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:07Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:05Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -456,7 +456,7 @@ build_info:
|
||||
output: "target/executable/multiqc"
|
||||
executable: "target/executable/multiqc/multiqc"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -636,9 +636,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
|
||||
|
||||
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component multiqc"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:02Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:22:59Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -398,7 +398,7 @@ build_info:
|
||||
output: "target/executable/pear"
|
||||
executable: "target/executable/pear/pear"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -596,9 +596,9 @@ echo "pear: $version" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Kai Waldrant"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component pear"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:06Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:04Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -277,7 +277,7 @@ build_info:
|
||||
output: "target/executable/salmon/salmon_index"
|
||||
executable: "target/executable/salmon/salmon_index/salmon_index"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
|
||||
|
||||
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:03Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:00Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -1173,7 +1173,7 @@ build_info:
|
||||
output: "target/executable/salmon/salmon_quant"
|
||||
executable: "target/executable/salmon/salmon_quant/salmon_quant"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
|
||||
|
||||
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:03Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:00Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -264,7 +264,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_collate"
|
||||
executable: "target/executable/samtools/samtools_collate/samtools_collate"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -243,7 +243,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_faidx"
|
||||
executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -433,7 +433,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_fasta"
|
||||
executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -433,7 +433,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_fastq"
|
||||
executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -173,7 +173,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_flagstat"
|
||||
executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -183,7 +183,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_idxstats"
|
||||
executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -189,7 +189,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_index"
|
||||
executable: "target/executable/samtools/samtools_index/samtools_index"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:08Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -332,7 +332,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_sort"
|
||||
executable: "target/executable/samtools/samtools_sort/samtools_sort"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:10Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:09Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -401,7 +401,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_stats"
|
||||
executable: "target/executable/samtools/samtools_stats/samtools_stats"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:09Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:07Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -665,7 +665,7 @@ build_info:
|
||||
output: "target/executable/samtools/samtools_view"
|
||||
executable: "target/executable/samtools/samtools_view/samtools_view"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:08Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:06Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -173,7 +173,7 @@ build_info:
|
||||
output: "target/executable/seqtk/seqtk_sample"
|
||||
executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.authors="Jakub Majercik"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:02Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -196,7 +196,7 @@ build_info:
|
||||
output: "target/executable/seqtk/seqtk_subseq"
|
||||
executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
|
||||
|
||||
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:02Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -2663,7 +2663,7 @@ build_info:
|
||||
output: "target/executable/star/star_align_reads"
|
||||
executable: "target/executable/star/star_align_reads/star_align_reads"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:03Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -333,7 +333,7 @@ build_info:
|
||||
output: "target/executable/star/star_genome_generate"
|
||||
executable: "target/executable/star/star_genome_generate/star_genome_generate"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:05Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:03Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -611,7 +611,7 @@ build_info:
|
||||
output: "target/executable/umi_tools/umi_tools_dedup"
|
||||
executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.authors="Emma Rousseau"
|
||||
LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:11Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:10Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -449,7 +449,7 @@ build_info:
|
||||
output: "target/executable/umi_tools/umi_tools_extract"
|
||||
executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -636,9 +636,9 @@ ENTRYPOINT []
|
||||
RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
|
||||
LABEL org.opencontainers.image.created="2024-07-29T07:58:12Z"
|
||||
LABEL org.opencontainers.image.created="2024-07-31T19:23:10Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
|
||||
LABEL org.opencontainers.image.revision="da414e72c60758895b16818309d6c147c288dd84"
|
||||
LABEL org.opencontainers.image.revision="8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -228,7 +228,7 @@ build_info:
|
||||
output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
|
||||
executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3042,7 +3042,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -706,7 +706,7 @@ build_info:
|
||||
output: "target/nextflow/arriba"
|
||||
executable: "target/nextflow/arriba/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3566,7 +3566,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/arriba",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -418,7 +418,7 @@ build_info:
|
||||
output: "target/nextflow/bcl_convert"
|
||||
executable: "target/nextflow/bcl_convert/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3303,7 +3303,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/bcl_convert",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -270,7 +270,7 @@ build_info:
|
||||
output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
|
||||
executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3116,7 +3116,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -232,7 +232,7 @@ build_info:
|
||||
output: "target/nextflow/bedtools/bedtools_getfasta"
|
||||
executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3060,7 +3060,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/bedtools/bedtools_getfasta",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
436
target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
Normal file
436
target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
Normal file
@@ -0,0 +1,436 @@
|
||||
name: "bedtools_intersect"
|
||||
namespace: "bedtools"
|
||||
version: "main"
|
||||
authors:
|
||||
- name: "Theodoro Gasperin Terra Camargo"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
links:
|
||||
email: "theodorogtc@gmail.com"
|
||||
github: "tgaspe"
|
||||
linkedin: "theodoro-gasperin-terra-camargo"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatician"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_a"
|
||||
alternatives:
|
||||
- "-a"
|
||||
description: "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
|
||||
info: null
|
||||
example:
|
||||
- "input_a.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input_b"
|
||||
alternatives:
|
||||
- "-b"
|
||||
description: "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
|
||||
info: null
|
||||
example:
|
||||
- "input_b.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "The output BED file. \n"
|
||||
info: null
|
||||
example:
|
||||
- "output.bed"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Options"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--write_a"
|
||||
alternatives:
|
||||
- "-wa"
|
||||
description: "Write the original A entry for each overlap."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_b"
|
||||
alternatives:
|
||||
- "-wb"
|
||||
description: "Write the original B entry for each overlap. \nUseful for knowing\
|
||||
\ _what_ A overlaps. Restricted by -f and -r.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--left_outer_join"
|
||||
alternatives:
|
||||
- "-loj"
|
||||
description: "Perform a \"left outer join\". That is, for each feature in A report\
|
||||
\ each overlap with B. \nIf no overlaps are found, report a NULL feature for\
|
||||
\ B.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_overlap"
|
||||
alternatives:
|
||||
- "-wo"
|
||||
description: "Write the original A and B entries plus the number of base pairs\
|
||||
\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
|
||||
\ \n Only A features with overlap are reported.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--write_overlap_plus"
|
||||
alternatives:
|
||||
- "-wao"
|
||||
description: "Write the original A and B entries plus the number of base pairs\
|
||||
\ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
|
||||
\ \n However, A features w/o overlap are also reported with a NULL B feature\
|
||||
\ and overlap = 0.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--report_A_if_no_overlap"
|
||||
alternatives:
|
||||
- "-u"
|
||||
description: "Write the original A entry _if_ no overlap is found. \n- In other\
|
||||
\ words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f\
|
||||
\ and -r. \n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--number_of_overlaps_A"
|
||||
alternatives:
|
||||
- "-c"
|
||||
description: "For each entry in A, report the number of overlaps with B.\n- Reports\
|
||||
\ 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f\
|
||||
\ and -r.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--report_no_overlaps_A"
|
||||
alternatives:
|
||||
- "-v"
|
||||
description: "Only report those entries in A that have _no overlaps_ with B.\n\
|
||||
- Similar to \"grep -v\" (an homage).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--uncompressed_bam"
|
||||
alternatives:
|
||||
- "-ubam"
|
||||
description: "Write uncompressed BAM output. Default writes compressed BAM."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--same_strand"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Require same strandedness. That is, only report hits in B.\nthat\
|
||||
\ overlap A on the _same_ strand.\n- By default, overlaps are reported without\
|
||||
\ respect to strand.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--opposite_strand"
|
||||
alternatives:
|
||||
- "-S"
|
||||
description: "Require different strandedness. That is, only report hits in B\n\
|
||||
that overlap A on the _opposite_ strand.\n- By default, overlaps are reported\
|
||||
\ without respect to strand.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "double"
|
||||
name: "--min_overlap_A"
|
||||
alternatives:
|
||||
- "-f"
|
||||
description: "Minimum overlap required as a fraction of A.\n- Default is 1E-9\
|
||||
\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
info: null
|
||||
example:
|
||||
- 0.5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--min_overlap_B"
|
||||
alternatives:
|
||||
- "-F"
|
||||
description: "Minimum overlap required as a fraction of B.\n- Default is 1E-9\
|
||||
\ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
info: null
|
||||
example:
|
||||
- 0.5
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--reciprocal_overlap"
|
||||
alternatives:
|
||||
- "-r"
|
||||
description: "Require that the fraction overlap be reciprocal for A AND B.\n-\
|
||||
\ In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap\
|
||||
\ 90% of A and A _also_ overlaps 90% of B.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--either_overlap"
|
||||
alternatives:
|
||||
- "-e"
|
||||
description: "Require that the minimum fraction be satisfied for A OR B.\n- In\
|
||||
\ other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either\
|
||||
\ 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would\
|
||||
\ have to be satisfied.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--split"
|
||||
description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "file"
|
||||
name: "--genome"
|
||||
alternatives:
|
||||
- "-g"
|
||||
description: "Provide a genome file to enforce consistent chromosome \nsort order\
|
||||
\ across input files. Only applies when used \nwith -sorted option.\n"
|
||||
info: null
|
||||
example:
|
||||
- "genome.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--nonamecheck"
|
||||
description: "For sorted data, don't throw an error if the file \nhas different\
|
||||
\ naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\"\
|
||||
).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--sorted"
|
||||
description: "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--names"
|
||||
description: "When using multiple databases, provide an alias \nfor each that\
|
||||
\ will appear instead of a fileId when \nalso printing the DB record.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--filenames"
|
||||
description: "When using multiple databases, show each complete filename instead\
|
||||
\ of a fileId when also printing the DB record."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--sortout"
|
||||
description: "When using multiple databases, sort the output DB hits for each\
|
||||
\ record."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--bed"
|
||||
description: "If using BAM input, write output as BED."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--header"
|
||||
description: "Print the header from the A file prior to results."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--no_buffer_output"
|
||||
alternatives:
|
||||
- "--nobuf"
|
||||
description: "Disable buffered output. Using this option will cause each line\n\
|
||||
of output to be printed as it is generated, rather than saved\nin a buffer.\
|
||||
\ This will make printing large output files \nnoticeably slower, but can be\
|
||||
\ useful in conjunction with\nother software tools and scripts that need to\
|
||||
\ process one\nline of bedtools output at a time.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--io_buffer_size"
|
||||
alternatives:
|
||||
- "--iobuf"
|
||||
description: "Specify amount of memory to use for input buffer.\nTakes an integer\
|
||||
\ argument. Optional suffixes K/M/G supported.\nNote: currently has no effect\
|
||||
\ with compressed files. \n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "bedtools intersect allows one to screen for overlaps between two sets\
|
||||
\ of genomic features. \nMoreover, it allows one to have fine control as to how\
|
||||
\ the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF\
|
||||
\ and BAM files as input.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
keywords:
|
||||
- "feature intersection"
|
||||
- "BAM"
|
||||
- "BED"
|
||||
- "GFF"
|
||||
- "VCF"
|
||||
license: "GPL-2.0, MIT"
|
||||
references:
|
||||
doi:
|
||||
- "10.1093/bioinformatics/btq033"
|
||||
links:
|
||||
repository: "https://github.com/arq5x/bedtools2"
|
||||
documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "bedtools"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "docker"
|
||||
run:
|
||||
- "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
|
||||
\ > /var/software_versions.txt\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/bedtools/bedtools_intersect/config.vsh.yaml"
|
||||
runner: "nextflow"
|
||||
engine: "docker|native"
|
||||
output: "target/nextflow/bedtools/bedtools_intersect"
|
||||
executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
version: "main"
|
||||
description: "A collection of bioinformatics tools for working with sequence data.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "modules"
|
||||
- "sequencing"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/biobox"
|
||||
issue_tracker: "https://github.com/viash-hub/biobox/issues"
|
||||
3884
target/nextflow/bedtools/bedtools_intersect/main.nf
Normal file
3884
target/nextflow/bedtools/bedtools_intersect/main.nf
Normal file
File diff suppressed because it is too large
Load Diff
126
target/nextflow/bedtools/bedtools_intersect/nextflow.config
Normal file
126
target/nextflow/bedtools/bedtools_intersect/nextflow.config
Normal file
@@ -0,0 +1,126 @@
|
||||
manifest {
|
||||
name = 'bedtools/bedtools_intersect'
|
||||
mainScript = 'main.nf'
|
||||
nextflowVersion = '!>=20.12.1-edge'
|
||||
version = 'main'
|
||||
description = 'bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n'
|
||||
author = 'Theodoro Gasperin Terra Camargo'
|
||||
}
|
||||
|
||||
process.container = 'nextflow/bash:latest'
|
||||
|
||||
// detect tempdir
|
||||
tempDir = java.nio.file.Paths.get(
|
||||
System.getenv('NXF_TEMP') ?:
|
||||
System.getenv('VIASH_TEMP') ?:
|
||||
System.getenv('TEMPDIR') ?:
|
||||
System.getenv('TMPDIR') ?:
|
||||
'/tmp'
|
||||
).toAbsolutePath()
|
||||
|
||||
profiles {
|
||||
no_publish {
|
||||
process {
|
||||
withName: '.*' {
|
||||
publishDir = [
|
||||
enabled: false
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
mount_temp {
|
||||
docker.temp = tempDir
|
||||
podman.temp = tempDir
|
||||
charliecloud.temp = tempDir
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
// docker.userEmulation = true
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
docker.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
podman {
|
||||
podman.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
shifter.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
shifter {
|
||||
shifter.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
charliecloud.enabled = false
|
||||
}
|
||||
charliecloud {
|
||||
charliecloud.enabled = true
|
||||
docker.enabled = false
|
||||
singularity.enabled = false
|
||||
podman.enabled = false
|
||||
shifter.enabled = false
|
||||
}
|
||||
}
|
||||
|
||||
process{
|
||||
withLabel: mem1gb { memory = 1000000000.B }
|
||||
withLabel: mem2gb { memory = 2000000000.B }
|
||||
withLabel: mem5gb { memory = 5000000000.B }
|
||||
withLabel: mem10gb { memory = 10000000000.B }
|
||||
withLabel: mem20gb { memory = 20000000000.B }
|
||||
withLabel: mem50gb { memory = 50000000000.B }
|
||||
withLabel: mem100gb { memory = 100000000000.B }
|
||||
withLabel: mem200gb { memory = 200000000000.B }
|
||||
withLabel: mem500gb { memory = 500000000000.B }
|
||||
withLabel: mem1tb { memory = 1000000000000.B }
|
||||
withLabel: mem2tb { memory = 2000000000000.B }
|
||||
withLabel: mem5tb { memory = 5000000000000.B }
|
||||
withLabel: mem10tb { memory = 10000000000000.B }
|
||||
withLabel: mem20tb { memory = 20000000000000.B }
|
||||
withLabel: mem50tb { memory = 50000000000000.B }
|
||||
withLabel: mem100tb { memory = 100000000000000.B }
|
||||
withLabel: mem200tb { memory = 200000000000000.B }
|
||||
withLabel: mem500tb { memory = 500000000000000.B }
|
||||
withLabel: mem1gib { memory = 1073741824.B }
|
||||
withLabel: mem2gib { memory = 2147483648.B }
|
||||
withLabel: mem4gib { memory = 4294967296.B }
|
||||
withLabel: mem8gib { memory = 8589934592.B }
|
||||
withLabel: mem16gib { memory = 17179869184.B }
|
||||
withLabel: mem32gib { memory = 34359738368.B }
|
||||
withLabel: mem64gib { memory = 68719476736.B }
|
||||
withLabel: mem128gib { memory = 137438953472.B }
|
||||
withLabel: mem256gib { memory = 274877906944.B }
|
||||
withLabel: mem512gib { memory = 549755813888.B }
|
||||
withLabel: mem1tib { memory = 1099511627776.B }
|
||||
withLabel: mem2tib { memory = 2199023255552.B }
|
||||
withLabel: mem4tib { memory = 4398046511104.B }
|
||||
withLabel: mem8tib { memory = 8796093022208.B }
|
||||
withLabel: mem16tib { memory = 17592186044416.B }
|
||||
withLabel: mem32tib { memory = 35184372088832.B }
|
||||
withLabel: mem64tib { memory = 70368744177664.B }
|
||||
withLabel: mem128tib { memory = 140737488355328.B }
|
||||
withLabel: mem256tib { memory = 281474976710656.B }
|
||||
withLabel: mem512tib { memory = 562949953421312.B }
|
||||
withLabel: cpu1 { cpus = 1 }
|
||||
withLabel: cpu2 { cpus = 2 }
|
||||
withLabel: cpu5 { cpus = 5 }
|
||||
withLabel: cpu10 { cpus = 10 }
|
||||
withLabel: cpu20 { cpus = 20 }
|
||||
withLabel: cpu50 { cpus = 50 }
|
||||
withLabel: cpu100 { cpus = 100 }
|
||||
withLabel: cpu200 { cpus = 200 }
|
||||
withLabel: cpu500 { cpus = 500 }
|
||||
withLabel: cpu1000 { cpus = 1000 }
|
||||
}
|
||||
|
||||
|
||||
400
target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json
Normal file
400
target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json
Normal file
@@ -0,0 +1,400 @@
|
||||
{
|
||||
"$schema": "http://json-schema.org/draft-07/schema",
|
||||
"title": "bedtools_intersect",
|
||||
"description": "bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n",
|
||||
"type": "object",
|
||||
"definitions": {
|
||||
|
||||
|
||||
|
||||
"inputs" : {
|
||||
"title": "Inputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"input_a": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file",
|
||||
"help_text": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"input_b": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\":\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)",
|
||||
"help_text": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\":\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"outputs" : {
|
||||
"title": "Outputs",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"output": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file",
|
||||
"help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n"
|
||||
,
|
||||
"default": "$id.$key.output.bed"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"options" : {
|
||||
"title": "Options",
|
||||
"type": "object",
|
||||
"description": "No description",
|
||||
"properties": {
|
||||
|
||||
|
||||
"write_a": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"write_b": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap. \nUseful for knowing _what_ A overlaps. Restricted by -f and -r.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"left_outer_join": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\"",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\". That is, for each feature in A report each overlap with B. \nIf no overlaps are found, report a NULL feature for B.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"write_overlap": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n Only A features with overlap are reported.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"write_overlap_plus": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"report_A_if_no_overlap": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found. \n- In other words, just report the fact \u003e=1 hit was found.\n- Overlaps restricted by -f and -r. \n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"number_of_overlaps_A": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"report_no_overlaps_A": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"uncompressed_bam": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output. Default writes compressed BAM."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"same_strand": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Require same strandedness",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Require same strandedness. That is, only report hits in B.\nthat overlap A on the _same_ strand.\n- By default, overlaps are reported without respect to strand.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"opposite_strand": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Require different strandedness",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Require different strandedness. That is, only report hits in B\nthat overlap A on the _opposite_ strand.\n- By default, overlaps are reported without respect to strand.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"min_overlap_A": {
|
||||
"type":
|
||||
"number",
|
||||
"description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A",
|
||||
"help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"min_overlap_B": {
|
||||
"type":
|
||||
"number",
|
||||
"description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B",
|
||||
"help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"reciprocal_overlap": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90% of A and A _also_ overlaps 90% of B.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"either_overlap": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would have to be satisfied.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"split": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"genome": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files",
|
||||
"help_text": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files. Only applies when used \nwith -sorted option.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"nonamecheck": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\").\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"sorted": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"names": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record",
|
||||
"help_text": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record.\n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"filenames": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"sortout": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"bed": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"header": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results."
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"no_buffer_output": {
|
||||
"type":
|
||||
"boolean",
|
||||
"description": "Type: `boolean_true`, default: `false`. Disable buffered output",
|
||||
"help_text": "Type: `boolean_true`, default: `false`. Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files \nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n"
|
||||
,
|
||||
"default": "False"
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"io_buffer_size": {
|
||||
"type":
|
||||
"integer",
|
||||
"description": "Type: `integer`. Specify amount of memory to use for input buffer",
|
||||
"help_text": "Type: `integer`. Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files. \n"
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
"nextflow input-output arguments" : {
|
||||
"title": "Nextflow input-output arguments",
|
||||
"type": "object",
|
||||
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
||||
"properties": {
|
||||
|
||||
|
||||
"publish_dir": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
||||
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
||||
|
||||
}
|
||||
|
||||
|
||||
,
|
||||
"param_list": {
|
||||
"type":
|
||||
"string",
|
||||
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
||||
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
||||
"hidden": true
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
},
|
||||
"allOf": [
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/inputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/outputs"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/options"
|
||||
},
|
||||
|
||||
{
|
||||
"$ref": "#/definitions/nextflow input-output arguments"
|
||||
}
|
||||
]
|
||||
}
|
||||
@@ -158,7 +158,7 @@ build_info:
|
||||
output: "target/nextflow/busco/busco_download_datasets"
|
||||
executable: "target/nextflow/busco/busco_download_datasets/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -2985,7 +2985,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/busco/busco_download_datasets",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -145,7 +145,7 @@ build_info:
|
||||
output: "target/nextflow/busco/busco_list_datasets"
|
||||
executable: "target/nextflow/busco/busco_list_datasets/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -2971,7 +2971,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/busco/busco_list_datasets",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -423,7 +423,7 @@ build_info:
|
||||
output: "target/nextflow/busco/busco_run"
|
||||
executable: "target/nextflow/busco/busco_run/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3283,7 +3283,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/busco/busco_run",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -740,7 +740,7 @@ build_info:
|
||||
output: "target/nextflow/cutadapt"
|
||||
executable: "target/nextflow/cutadapt/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
@@ -3593,7 +3593,7 @@ meta = [
|
||||
"engine" : "docker|native",
|
||||
"output" : "target/nextflow/cutadapt",
|
||||
"viash_version" : "0.9.0-RC6",
|
||||
"git_commit" : "da414e72c60758895b16818309d6c147c288dd84",
|
||||
"git_commit" : "8f525f5e40301ad51bc1cd9587c0febbef84bd7d",
|
||||
"git_remote" : "https://github.com/viash-hub/biobox"
|
||||
},
|
||||
"package_config" : {
|
||||
|
||||
@@ -317,7 +317,7 @@ build_info:
|
||||
output: "target/nextflow/falco"
|
||||
executable: "target/nextflow/falco/main.nf"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "da414e72c60758895b16818309d6c147c288dd84"
|
||||
git_commit: "8f525f5e40301ad51bc1cd9587c0febbef84bd7d"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user