modules/instrain_compare

Strain-level comparisons across multiple inStrain profiles

instraincomparealigndiversitycoverage

https://github.com/nf-core/modules/[...]/modules/nf-core/instrain/compare

Description

Strain-level comparisons across multiple inStrain profiles

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`bams`
`:file`

Path to .bam files that were profiled

*.{bam,sam}

`profiles`
`:directory`

InStrain profile folders

*.IS/

`stb_file`
`:file`

Path to .stb (scaffold to bin) file that was profiled

*.stb

Output

name:type

description

pattern

`compare`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`*.IS_compare`
`:directory`

inStrain compare folders

*.IS_compare/

`comparisons_table`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`.IS_compare/output/.IS_compare_comparisonsTable.tsv`
`:file`

Comparisons table

*.tsv

`pooled_snv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`.IS_compare/output/.IS_compare_pooled_SNV_data.tsv`
`:file`

Pooled SNV

*.tsv

`snv_keys`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`.IS_compare/output/.IS_compare_pooled_SNV_data_keys.tsv`
`:file`

SNV keys

*.tsv

`snv_info`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`.IS_compare/output/.IS_compare_pooled_SNV_info.tsv`
`:file`

SNV information

*.tsv

`versions_instrain`

`${task.process}`
`:string`

The name of the process

`instrain`
`:string`

The name of the tool

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`instrain`
`:string`

The name of the tool

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

The expression to obtain the version of the tool

Tools

instrain
MIT

Calculation of strain-level metrics

github.com/MrOlm/instrain instrain.readthedocs.io/en/latest https://github.com/MrOlm/instrain 10.1038/s41587-020-00797-0

modules/instrain_compare

Description

Input

`meta`
`:map`

`bams`
`:file`

`profiles`
`:directory`

`stb_file`
`:file`

Output

`compare`

`meta`
`:map`

`*.IS_compare`
`:directory`

`comparisons_table`

`meta`
`:map`

`.IS_compare/output/.IS_compare_comparisonsTable.tsv`
`:file`

`pooled_snv`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_data.tsv`
`:file`

`snv_keys`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_data_keys.tsv`
`:file`

`snv_info`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_info.tsv`
`:file`

`versions_instrain`

`${task.process}`
`:string`

`instrain`
`:string`

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`instrain`
`:string`

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

Tools

instrain
MIT

included in

maintainers

get in touch

modules/instrain_compare

Description

Input

meta:map

bams:file

profiles:directory

stb_file:file

Output

compare

meta:map

*.IS_compare:directory

comparisons_table

meta:map

*.IS_compare/output/*.IS_compare_comparisonsTable.tsv:file

pooled_snv

meta:map

*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv:file

snv_keys

meta:map

*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv:file

snv_info

meta:map

*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv:file

versions_instrain

${task.process}:string

instrain:string

inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p':eval

Topics

versions

${task.process}:string

instrain:string

inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p':eval

Tools

instrain MIT

included in

maintainers

get in touch

`meta`
`:map`

`bams`
`:file`

`profiles`
`:directory`

`stb_file`
`:file`

`compare`

`meta`
`:map`

`*.IS_compare`
`:directory`

`comparisons_table`

`meta`
`:map`

`.IS_compare/output/.IS_compare_comparisonsTable.tsv`
`:file`

`pooled_snv`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_data.tsv`
`:file`

`snv_keys`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_data_keys.tsv`
`:file`

`snv_info`

`meta`
`:map`

`.IS_compare/output/.IS_compare_pooled_SNV_info.tsv`
`:file`

`versions_instrain`

`${task.process}`
`:string`

`instrain`
`:string`

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

`versions`

`${task.process}`
`:string`

`instrain`
`:string`

`inStrain compare --version 2>&1 | sed -n 's/.*inStrain version //p'`
`:eval`

instrain
MIT