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momps and mlst: remove collect from report to avoid overwriting previous results when a pipeline is resumed #196

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momps and mlst: remove collect from report to avoid overwriting previous results when a pipeline is resumed #196

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50be919
momps and mlst processes now compile results per sample to avoid
cimendes Feb 18, 2019
82eef75
update changelog
cimendes Feb 18, 2019
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3 changes: 3 additions & 0 deletions changelog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@ all the components.
position in the `nextflow run` command inside the .nextflow.log file.
- Fix parsing of .nextflow.log file when searching for `nextflow run` command.
- Fixed bug between mash_sketch_fasta and mash_dist.
- `momps` and `mlst` components now save results per sample to avoid overwriting
results from previous runs

### Minor/Other changes

Expand All @@ -30,6 +32,7 @@ with a secondary channel into `mafft`
- New version of DEN-IM recipe
- Now prints an ordered list of components
- Moved taxonomy results from `results/annotation/` to `results/taxonomy/`
- Moved mlst results from `results/annotation/` to `results/typing/`


## 1.4.0
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10 changes: 5 additions & 5 deletions flowcraft/generator/templates/mlst.nf
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Expand Up @@ -12,7 +12,7 @@ process mlst_{{ pid }} {
set sample_id, file(assembly) from {{ input_channel }}

output:
file '*.mlst.txt' into LOG_mlst_{{ pid }}
set sample_id, file('*.mlst.txt') into LOG_mlst_{{ pid }}
set sample_id, file(assembly), file(".status") into MAIN_mlst_out_{{ pid }}
{% with task_name="mlst" %}
{%- include "compiler_channels.txt" ignore missing -%}
Expand Down Expand Up @@ -47,17 +47,17 @@ process mlst_{{ pid }} {

process compile_mlst_{{ pid }} {
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If the results are being produced for each sample, then the whole compile_mlst process is not needed anymore. You could just remove this process and add the publishDir of the appropriate output in the mlst process correct?

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If for some reason, this process in kept, then the name does not make sense anymore, as it is not compiling stuff.


publishDir "results/annotation/mlst_{{ pid }}/"
publishDir "results/typing/mlst_{{ pid }}/"

input:
file res from LOG_mlst_{{ pid }}.collect()
set sample_id, res from LOG_mlst_{{ pid }}

output:
file "mlst_report.tsv"
file "*mlst_report.tsv"

script:
"""
cat $res >> mlst_report.tsv
cat $res > ${sample_id}_mlst_report.tsv
"""
}

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10 changes: 6 additions & 4 deletions flowcraft/generator/templates/momps.nf
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Expand Up @@ -14,6 +14,7 @@ process momps_{{ pid }} {
val clear from checkpointClear_{{ pid }}

output:
val sample_id into momps_sample_id_{{ pid }}
file("*_st.tsv") into momps_st_{{ pid }}
file("*_profile.tsv") into momps_profile_{{ pid }}
{% with task_name="momps" %}
Expand Down Expand Up @@ -75,17 +76,18 @@ process momps_report_{{ pid }} {
publishDir "results/typing/momps_{{ pid }}/", pattern: "*.tsv"

input:
file(st_file) from momps_st_{{ pid }}.collect()
file(profile_file) from momps_profile_{{ pid }}.collect()
val sample_id from momps_sample_id_{{ pid }}
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The same login applies here. If output is not being compile, then it makes more sense to just create these files on the main process and move the publishDir there.

file(st_file) from momps_st_{{ pid }}
file(profile_file) from momps_profile_{{ pid }}

output:
file "*.tsv"


script:
"""
cat $st_file >> momps_st.tsv
cat $profile_file >> momps_profile.tsv
cat $st_file > ${sample_id}_momps_st.tsv
cat $profile_file > ${sample_id}_momps_profile.tsv
"""

}
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