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add output structure #23

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Jan 25, 2025
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add output structure #23

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22ac4aa
extra check for nglmr to avoid paired end data
Juke34 Jan 25, 2025
3338c37
add output structure information
Juke34 Jan 25, 2025
1d1193f
fix output that was not published in outdir
Juke34 Jan 25, 2025
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58 changes: 58 additions & 0 deletions README.md
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Expand Up @@ -21,6 +21,7 @@ AliNe is a pipeline written in Nextflow that aims to efficiently align reads aga
* [Singularity](#singularity)
* [Usage and test](#usage)
* [Parameters](#parameters)
* [Output](#output)
* [Contributing](#contributing)

## Foreword
Expand Down Expand Up @@ -350,6 +351,63 @@ On success you should get a message looking like this:
--sublong_options additional options for sublong
```

## Output

Here the description of typical ouput you will get from AliNe:

```
└── alignment_results # Output folder set using --outdir. Default: <alignment_results>
│
├── fastp # Folder - trimming with fastp (optional - if trimming activated by the user)
│ ├── sample1_fastp_report.html # fastp report for sample1
│ └── sample1_seqkit_trim.fastq.gz # sample1 trimmed fastq file
│
├── seqkit_score # Folder containing Sequencing scoring system detected with Seqkit
│ └── sample1.result.txt # Information about scoring system detected in sample1 (Phred+33, Phred+64 and Solexa), and change applied
│
├── mean_read_length # Folder with mean read length computed in bash (optional - done if selected aligners need the info and no value provided by the user)
│ └── sample1_seqkit_trim_sampled_read_length.txt # Mean read length for sample1
│
├── salmon_libtype # Librairy information (read orientation and strand information) detected via Salmon
│ └── sample1_lib_format_counts.json # Librairy information detectected for sample1
|
├── alignment # Folder gathering all alignment output (indicies, sorted bam and logs)
│ ├── aligner1 # Folder gathering data produced by aligner
│ │ ├── indicies # Contains the genome index for the aligner
│ │ │ └── ... #
│ │ ├── sample1_seqkit_trim_aligner1_sorted.log # Ccontains the log of the aligner
│ │ └── sample1_seqkit_trim_aligner1_sorted.bam # Sorted bam output
│ └── aligner2 # Folder gathering data produced by aligner
│ ├── indicies # Contains the genome index for the aligner
│ │ └── ... #
│ ├── sample1_seqkit_trim_aligner2_sorted.log # Contains the log of the aligner
│ └── sample1_seqkit_trim_aligner2_sorted.bam # Sorted bam output
│
├── fastqc # FastQC statistics folder
│ ├── raw # Folder with FastQC result for raw data
│ │ └── fastqc_sample1_raw_logs # Folder with FastQC result for raw sample1 data
│ │ ├── sample1_fastqc.html # FastQC interactive file summarizing the results of the analysis, with graphs and interpretations.
│ │ └── sample1_fastqc.zip # Contains all the detailed data and graphics generated by FastQC
│ └── trimming_fastp # Folder with FastQC result for trimmed data (optional - if trimming activated by the user)
│ │ └── fastqc_sample1_trimmed_logs # FastQC output folder for trimmed sample1 data
│ │ ├── sample1_seqkit_trim_fastqc.html # FastQC interactive file summarizing the results of the analysis, with graphs and interpretations.
│ │ └── sample1_seqkit_trim_fastqc.zip # Contains all the detailed data and graphics generated by FastQC
│ ├── aligner1 # FastQC output folder for data aligned with aligner1
│ │ └── fastqc_sample1_aligner1_logs # FastQC output folder for sample1 data aligned with aligner1
│ │ ├── sample1_seqkit_trim_aligner1_sorted_fastqc.html # FastQC interactive file summarizing the results of the analysis, with graphs and interpretations.
│ │ └── sample1_seqkit_trim_aligner1_sorted_fastqc.zip # Contains all the detailed data and graphics generated by FastQC
│ └── aligner2 # FastQC output folder for data aligned with aligner2
│ └── fastqc_sample1_aligner2_logs # FastQC output folder for sample1 data aligned with aligner2
│ ├── sample1_seqkit_trim_aligner2_sorted_fastqc.html # FastQC interactive file summarizing the results of the analysis, with graphs and interpretations.
│ └── sample1_seqkit_trim_aligner2_sorted_fastqc.zip # Contains all the detailed data and graphics generated by FastQC
│
└── MultiQC # MultiQC folder that aggregate results across many samples into a single report
├── multiqc_report.html # Report with interactive plots for statistics across many samples.
└── multiqc_report_data # Plot and data used by the multiqc_report.html

```


## Contributing

Contributions from the community are welcome ! See the [Contributing guidelines](https://github.com/Juke34/aline/blob/main/CONTRIBUTING.md)
6 changes: 5 additions & 1 deletion aline.nf
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Expand Up @@ -255,6 +255,10 @@ if ("ngmlr" in aligner_list ){
//stop_pipeline = true
//}
}
if ( params.read_type == "short_paired"){
log.error "ngmlr aligner does not handle paired reads, please remove it from the list of aligner to use.\n"
stop_pipeline = true
}
}

// novoalign tool - load license into the container
Expand Down Expand Up @@ -565,7 +569,7 @@ workflow align {
if (params.library_type.contains("auto")){
// ------------------- guess libtype -------------------
salmon_index(genome.collect())
salmon_guess_lib(seqtk_sample.out.sampled, salmon_index.out.index, "salmon")
salmon_guess_lib(seqtk_sample.out.sampled, salmon_index.out.index, "salmon_libtype")
salmon_guess_lib.out.tuple_id_libtype.set{tuple_id_lib}
} else {
set_tuple_withUserLib(raw_reads_trim)
Expand Down
6 changes: 4 additions & 2 deletions modules/salmon.nf
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Expand Up @@ -20,7 +20,7 @@ process salmon_index {

process salmon_guess_lib {
label 'salmon'
publishDir "${params.outdir}/${outpath}", pattern: "*", mode: 'copy'
publishDir "${params.outdir}/${outpath}", pattern: "*/*.json", mode: 'copy'

input:
tuple val(id), path(fastq)
Expand All @@ -29,7 +29,7 @@ process salmon_guess_lib {

output:
tuple val(id), env(LIBTYPE), emit: tuple_id_libtype

path "*/*lib_format_counts.json"

script:

Expand All @@ -44,6 +44,8 @@ process salmon_guess_lib {
salmon quant -i ${salmon_index} -l A ${input} --thread ${task.cpus} -o ${output} --minAssignedFrags 2
# extract the result
LIBTYPE=\$(grep expected_format ${output}/lib_format_counts.json | awk '{print \$2}' | tr -d '",\n')
# change output name
mv ${output}/lib_format_counts.json ${output}/${id}_lib_format_counts.json
"""

}
Expand Down
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