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Merge pull request #233 from UPHL-BioNGS/update-2023-09-26
Update 2023 09 26
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| Original file line number | Diff line number | Diff line change |
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@@ -19,8 +19,7 @@ jobs: | |
| 'ncov_V4', | ||
| 'ncov_V4.1', | ||
| 'ncov_V5.3.2', | ||
| 'mpx_primalseq', | ||
| 'mpx_idt' | ||
| 'mpx_primalseq' | ||
| ] | ||
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| steps: | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,82 @@ | ||
| #!/bin/bash | ||
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| ##### ##### ##### ##### ##### ##### ##### ##### ##### | ||
| # It's like nf-core's version, but jankier ##### | ||
| ##### ##### ##### ##### ##### ##### ##### ##### ##### | ||
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| # this | ||
| # 1. finds all the params | ||
| # 2. checks that they are in nextflow_schema.json | ||
| # 3. checks that their default value is in nextflow_schema.json | ||
| # 4. checks that every param and its default value is in the config file | ||
| # 5. checks that every process with its default values are in the config file | ||
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| ##### ##### ##### ##### ##### ##### ##### ##### ##### | ||
| # finding all the params ##### | ||
| ##### ##### ##### ##### ##### ##### ##### ##### ##### | ||
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| params=$(grep param main.nf | awk '{ ( $1=$1 ) ; print $0 }' | grep ^param | awk '{print $1}' | sort | uniq | cut -f 2 -d '.') | ||
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| for param in ${params[@]} | ||
| do | ||
| echo "evaluating params.$param" | ||
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| # default value | ||
| default="$(grep -w params.$param main.nf | grep "=" | head -n 1 | sed 's/.*=//g' | awk '{ ( $1=$1 ) ; print $0 }' ) " | ||
| echo -e "default:\t$default" | ||
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| # 2. checks that they are in nextflow_schema.json | ||
| schema_check=$(grep "\"$param\":" nextflow_schema.json | head -n 1) | ||
| if [ -n "$schema_check" ] | ||
| then | ||
| # 3. checks that their default value is in nextflow_schema.json | ||
| schema_default="$(grep "\"$param\":" -A 10 nextflow_schema.json | grep "}" -B 10 -m 1 | grep "default" | head -n 1 | sed 's/.*://g' | awk '{ ( $1=$1 ) ; print $0 }' )" | ||
| echo -e "schema:\t\t$schema_default" | ||
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| else | ||
| echo "$param was not included in nextflow_schema.json file!!!" | ||
| fi | ||
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| config_check=$(grep "params.$param =" configs/cecret_config_template.config | head -n 1) | ||
| if [ -n "$config_check" ] | ||
| then | ||
| # 4. checks that every param and its default value is in the config file | ||
| config_default="$(grep -w params.$param configs/cecret_config_template.config | grep -v "#" | head -n 1 | sed 's/.*=//g' | awk '{ ( $1=$1 ) ; print $0 }' )" | ||
| echo -e "config:\t\t$config_default" | ||
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| else | ||
| echo "$param was not included in configs/cecret_config_template.config file!!!" | ||
| fi | ||
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| echo "" | ||
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| done | ||
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| echo "##### ##### ##### ##### #####" | ||
| echo "# Now for the processes #####" | ||
| echo "##### ##### ##### ##### #####" | ||
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| processes=$(grep ^process -h modules/*nf | awk '{print $2}' | sort | uniq ) | ||
| echo ${processes[@]} | ||
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| for process in ${processes[@]} | ||
| do | ||
| #echo "getting information for $process" | ||
| #grep "process $process {" -h modules/*nf -A 200 | grep -e "when:" -e "input:" -B 200 -m 1 | grep -v "#UPHLICA" | grep -v "when:" | grep -v "input:" | grep -v "tag" | ||
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| echo -e "//\twithName:$process{" | ||
| while read line | ||
| do | ||
| key=$(echo $line | awk '{print $1}' | grep -v process ) | ||
| if [ -n "$key" ] | ||
| then | ||
| value=$(echo $line | sed "s|$key||g" | awk '{ ( $1=$1 ) ; print $0 }' | sed 's/\"${params.outdir}\"/cecret/g') | ||
| echo -e "//\t\t$key = \"$value\"" | ||
| fi | ||
| done < <(grep "process $process {" -h modules/*nf -A 200 | grep -e "when:" -e "input:" -B 200 -m 1 | grep -v "#UPHLICA" | grep -v "when:" | grep -v "input:" | grep -v "tag") | ||
| echo -e "//\t}" | ||
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| #echo "" | ||
| #grep "// withName:$process{" -A 20 configs/cecret_config_template.config | grep -m 1 "}" -B 20 | ||
| done |
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