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Merge pull request #126 from nasa/DEV_NF_MAAgilent_1ch
Microarray Agilent 1-channel workflow updates from v 1.0.3 to 1.0.4
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17 changes: 17 additions & 0 deletions
17
...mentation/NF_MAAgilent1ch/workflow_code/modules/POST_PROCESSING/GENERATE_PROTOCOL/main.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| process GENERATE_PROTOCOL { | ||
| tag "${ params.gldsAccession }" | ||
| publishDir "${ params.outputDir }/${ params.gldsAccession }/GeneLab", | ||
| mode: params.publish_dir_mode | ||
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| input: | ||
| path("software_versions_GLmicroarray.md") | ||
| val(organism) | ||
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| output: | ||
| path("PROTOCOL_GLmicroarray.txt") | ||
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| script: | ||
| """ | ||
| generate_protocol.sh $workflow.manifest.version \"$organism\" | ||
| """ | ||
| } |
68 changes: 68 additions & 0 deletions
68
...low_code/modules/POST_PROCESSING/GENERATE_PROTOCOL/resources/usr/bin/generate_protocol.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| #!/bin/bash | ||
| set -u | ||
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| software_versions_file="software_versions_GLmicroarray.md" | ||
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| # Read the markdown table | ||
| while read -r line; do | ||
| # Extract program, version, and link | ||
| program=$(echo "$line" | awk -F'|' '{gsub(/^[[:blank:]]+|[[:blank:]]+$/,"",$1); print $1}') | ||
| version=$(echo "$line" | awk -F'|' '{gsub(/^[[:blank:]]+|[[:blank:]]+$/,"",$2); print $2}') | ||
|
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| # Skip the header row and rows without version information | ||
| if [[ $program != "Program" && $version != "Version" && ! -z $version ]]; then | ||
| # Replace invalid characters in program name with underscores | ||
| sanitized_program=$(echo "$program" | tr -cd '[:alnum:]_') | ||
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| # Create environment variable name | ||
| env_var_name="${sanitized_program}_VERSION" | ||
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| # Set the environment variable | ||
| export "$env_var_name=$version" | ||
| fi | ||
| done < <(sed -n '/|/p' "$software_versions_file" | sed 's/^ *|//;s/|$//') | ||
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| # Print the extracted versions | ||
| env | grep "_VERSION" | ||
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| # Get organism | ||
| organism=$2 | ||
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| # List of organisms | ||
| organism_list=("Homo sapiens" "Mus musculus" "Rattus norvegicus" "Drosophila melanogaster" "Caenorhabditis elegans" "Danio rerio" "Saccharomyces cerevisiae") | ||
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| # Check the value of 'organism' variable and set 'GENE_MAPPING_STEP' accordingly | ||
| if [[ $organism == "Arabidopsis thaliana" ]]; then | ||
| GENE_MAPPING_STEP="Ensembl gene ID mappings were retrieved for each probe using the Plants Ensembl database ftp server (plants.ensembl.org, release 54)." | ||
| elif [[ " ${organism_list[*]} " == *"${organism//\"/}"* ]]; then | ||
| GENE_MAPPING_STEP="Ensembl gene ID mappings were retrieved for each probe using biomaRt (version ${biomaRt_VERSION}), Ensembl database (ensembl.org, release 107)." | ||
| else | ||
| GENE_MAPPING_STEP="TBD" | ||
| fi | ||
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| # Check the value of 'organism' variable and set 'GENE_ANNOTATION_DB' accordingly | ||
| if [[ $organism == "Arabidopsis thaliana" ]]; then | ||
| GENE_ANNOTATION_DB="org.At.tair.db" | ||
| elif [[ $organism == "Homo sapiens" ]]; then | ||
| GENE_ANNOTATION_DB="org.Hs.eg.db" | ||
| elif [[ $organism == "Mus musculus" ]]; then | ||
| GENE_ANNOTATION_DB="org.Mm.eg.db" | ||
| elif [[ $organism == "Rattus norvegicus" ]]; then | ||
| GENE_ANNOTATION_DB="org.Rn.eg.db" | ||
| elif [[ $organism == "Drosophila melanogaster" ]]; then | ||
| GENE_ANNOTATION_DB="org.Dm.eg.db" | ||
| elif [[ $organism == "Caenorhabditis elegans" ]]; then | ||
| GENE_ANNOTATION_DB="org.Ce.eg.db" | ||
| elif [[ $organism == "Danio rerio" ]]; then | ||
| GENE_ANNOTATION_DB="org.Dr.eg.db" | ||
| elif [[ $organism == "Saccharomyces cerevisiae" ]]; then | ||
| GENE_ANNOTATION_DB="org.Sc.sgd.db" | ||
| else | ||
| GENE_ANNOTATION_DB="TBD" | ||
| fi | ||
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| # Read the template file | ||
| template="Data were processed as described in GL-DPPD-7112 ([https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Agilent_1-channel/Pipeline_GL-DPPD-7112_Versions/GL-DPPD-7112.md]), using NF_MAAgilent1ch version $1 ([https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAgilent1ch_$1/Microarray/Agilent_1-channel/Workflow_Documentation/NF_MAAgilent1ch]). In short, a RunSheet containing raw data file location and processing metadata from the study's *ISA.zip file was generated using dp_tools (version ${dp_tools_VERSION}). The raw array data files were loaded into R (version ${R_VERSION}) using limma (version ${limma_VERSION}). Raw data quality assurance density, pseudo image, MA, and foreground-background plots were generated using limma (version ${limma_VERSION}), and boxplots were generated using ggplot2 (version ${ggplot2_VERSION}). The raw intensity data was background corrected and normalized across arrays via the limma (version ${limma_VERSION}) quantile method. Normalized data quality assurance density, pseudo image, and MA plots were generated using limma (version ${limma_VERSION}), and boxplots were generated using ggplot2 (version ${ggplot2_VERSION}). ${GENE_MAPPING_STEP} Differential expression analysis was performed in R (version ${R_VERSION}) using limma (version ${limma_VERSION}); all groups were compared pairwise for each probe to generate a moderated t-statistic and associated p- and adjusted p-value. Gene annotations were assigned using the custom annotation tables generated in-house as detailed in GL-DPPD-7110 ([https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md]), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and ${GENE_ANNOTATION_DB} (version 3.15.0)." | ||
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| # Output the filled template | ||
| echo "$template" > PROTOCOL_GLmicroarray.txt |
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