diff --git a/workflows/paleogenomics/adna-analysis/README.md b/workflows/paleogenomics/adna-analysis/README.md index df53610a4c..752366cf50 100644 --- a/workflows/paleogenomics/adna-analysis/README.md +++ b/workflows/paleogenomics/adna-analysis/README.md @@ -7,10 +7,7 @@ The pipeline processes the sequencing-read input provided to the workflow togeth ## Required & Optional Inputs To run this workflow successfully, you need to provide the following input datasets and parameters: -* **`Choose Read Type` :** Select whether your input is Single-End or Paired-End. -* **`Input Single-end reads` :** Input single-end FASTQ reads (list collection) for the sample. -* **`Input Paired-end Forward reads (R1)` :** Input paired-end forward FASTQ reads (list collection) for the sample. -* **`Input Paired-end reverse reads (R2)` :** Input paired-end reverse FASTQ reads (list collection) for the sample. +* **`Input FASTQ reads` :** Input FASTQ reads for the sample, as a list of paired or unpaired reads (a `list:paired_or_unpaired` collection). Each element of the list is either a pair of forward and reverse reads or a single unpaired dataset, so single-end and paired-end samples are given to the workflow the same way — and a single run may mix both. Galaxy routes each element down the appropriate trimming and mapping path automatically, so no read-type parameter is needed. * **`Reference genome` :** Reference genome sequence in FASTA format. This is essential for read mapping and variant calling. * **`Choose Mapper` :** Switch to select the alignment tool. Choose between BWA and Bowtie2. * **`HapMap chromosome X reference` :** Optional HapMap dataset used for X-chromosome contamination estimation in ANGSD (used only if provided). diff --git a/workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml b/workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml index 09d85de465..d902c743db 100644 --- a/workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml +++ b/workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml @@ -1,14 +1,17 @@ - doc: Test outline for adna-analysis.ga (Single-End, BWA, No BED, HapMap Present) job: - Choose Read Type: Single-End - Input Single-end reads: + Input FASTQ reads: class: Collection - collection_type: list + collection_type: list:paired_or_unpaired elements: - - class: File + - class: Collection identifier: NIST7035 - location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz - filetype: fastqsanger.gz + collection_type: paired_or_unpaired + elements: + - class: File + identifier: unpaired + location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz + filetype: fastqsanger.gz Reference genome: class: File location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz @@ -54,7 +57,7 @@ mapDamage Visualisation: element_tests: NIST7035: - element_tests: + elements: dnacomp: asserts: has_text: @@ -66,11 +69,9 @@ has_text: text: "freeBayes" ANGSD report of nuclear contamination estimation: - element_tests: - NIST7035: - asserts: - has_text: - text: "Method1_MOM_estimate" + asserts: + has_text: + text: "Method1_MOM_estimate" Bcftools variant calling summary statistics report: element_tests: NIST7035: @@ -92,23 +93,22 @@ - doc: Test outline for adna-analysis.ga (Paired-End, Bowtie2, BED Present, No HapMap) job: - Choose Read Type: Paired-End - Input Paired-end Forward reads (R1): - class: Collection - collection_type: list - elements: - - class: File - identifier: NIST7035 - location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz - filetype: fastqsanger.gz - Input Paired-end reverse reads (R2): + Input FASTQ reads: class: Collection - collection_type: list + collection_type: list:paired_or_unpaired elements: - - class: File + - class: Collection identifier: NIST7035 - location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz - filetype: fastqsanger.gz + collection_type: paired_or_unpaired + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz + filetype: fastqsanger.gz + - class: File + identifier: reverse + location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz + filetype: fastqsanger.gz Reference genome: class: File location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz @@ -154,7 +154,7 @@ mapDamage Visualisation: element_tests: NIST7035: - element_tests: + elements: dnacomp: asserts: has_text: diff --git a/workflows/paleogenomics/adna-analysis/adna-analysis.ga b/workflows/paleogenomics/adna-analysis/adna-analysis.ga index e89d090c5f..b6067f8004 100644 --- a/workflows/paleogenomics/adna-analysis/adna-analysis.ga +++ b/workflows/paleogenomics/adna-analysis/adna-analysis.ga @@ -11,126 +11,45 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", "name": "Ancient DNA analysis", - "readme": "# Ancient DNA analysis pipeline\nThis workflow performs an ancient DNA (aDNA) based analysis similar to the one in the [nf-core/eager](https://nf-co.re/eager/2.5.3/) workflow. nf-core/eager is a bioinformatics best-practice processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.\n\nThe pipeline processes the sequencing-read input provided to the workflow together with a reference genome and optional supporting reference data. It aligns reads and performs extensive general NGS and aDNA-specific quality control on the results.\n\n\n## Required & Optional Inputs\nTo run this workflow successfully, you need to provide the following input datasets and parameters:\n\n* **`Choose Read Type` :** Select whether your input is Single-End or Paired-End.\n* **`Input Single-end reads` :** Input single-end FASTQ reads (list collection) for the sample.\n* **`Input Paired-end Forward reads (R1)` :** Input paired-end forward FASTQ reads (list collection) for the sample.\n* **`Input Paired-end reverse reads (R2)` :** Input paired-end reverse FASTQ reads (list collection) for the sample.\n* **`Reference genome` :** Reference genome sequence in FASTA format. This is essential for read mapping and variant calling.\n* **`Choose Mapper` :** Switch to select the alignment tool. Choose between BWA and Bowtie2.\n* **`HapMap chromosome X reference` :** Optional HapMap dataset used for X-chromosome contamination estimation in ANGSD (used only if provided).\n* **`Input Mitochondrial Chromosome Name` :** The exact header name of the mitochondrial chromosome in your reference FASTA file (e.g., MT, chrM, rCRS).\n* **`Kraken2 database directory` :** The database directory required for Kraken2 taxonomic classification.\n* **`Optional BED file for Sex.DetERRmine` :** An optional BED file containing specific genomic coordinates to restrict the Sex.DetERRmine analysis. Leave empty for standard whole-genome human analysis, or provide targeted regions to enable gender estimation for non-human organisms.\n* **`ANGSD region parameter` :** The specific genomic region to restrict the ANGSD analysis (e.g. 'X:5000000-154900000' for human male nuclear contamination estimation; adjust for your reference).\n\n\n## Workflow Steps\nBy default the pipeline currently performs the following:\n\n## 1. Preprocessing and Quality Control\n* **Quality Control:** Evaluates read quality before and after trimming (`FastQC`)\n* **Adapter Trimming:** Removes adapter sequences (`AdapterRemoval`)\n\n## 2. Read Mapping and Processing\n* **Alignment:** Maps reads to the provided reference genome conditionally using either (`BWA`) or (`Bowtie2`) based on user selection\n* **Filtering and Statistics:** Separates unmapped reads and calculates alignment statistics (`Samtools View and Flagstat`)\n* **Duplicate Removal:** Detects and marks PCR duplicates (`Picard MarkDuplicates`)\n* **Alignment Quality:** Generates detailed BAM quality metrics (`QualiMap BamQC`)\n* **Library Complexity:** Estimates library complexity (`Preseq`)\n\n## 3. Ancient DNA (aDNA) Analysis\n* **Damage Profiling:** Visualizes aDNA-specific C-to-T damage patterns (`mapDamage`)\n* **Endogenous Content:** Calculates the proportion of endogenous (target) DNA in the sample (`EndorSpy`)\n* **(`Optional`) Contamination:** Estimates nuclear X-chromosome contamination conditionally if HapMap data is provided (`ANGSD X-Contamination`)\n\n## 4. Biological Information\n* **Sex Determination:** Determines biological sex based on relative chromosome coverage ratio. This step adapts conditionally whether an optional BED file is provided (`Sex.DetERRmine`)\n* **Mt/Nuc Ratio:** Calculates the ratio of mitochondrial reads to nuclear reads utilizing the specified mitochondrial chromosome name (`MtNucRatioCalculator`)\n\n## 5. Genotyping\n* **Variant Analysis:** Performs variant calling to generate VCF files (`FreeBayes`)\n* **Variant Statistics:** Calculates statistics for the generated variants (`Bcftools stats`)\n\n## 6. Metagenomic Screening (For Unmapped Reads)\n* **Read Extraction:** Extracts unmapped reads for microbial analysis (`Picard SamToFastq`)\n* **Quality Filter:** Filters low-complexity sequences (`BBTools BBduk`)\n* **Taxonomic Classification:** Performs microbiome/taxonomic screening on the filtered unmapped reads (`Kraken2`)\n\n## 7. Reporting\n* **Summary Report:** Aggregates logs and statistics from all these tools into a single interactive HTML report (`MultiQC`)\n\n\n## Workflow Outputs\nUpon successful execution, the workflow explicitly provides the following final files for analysis:\n\n* **`MultiQC aggregated workflow summary report` :** An interactive HTML report aggregating QC and analysis logs from all tools.\n* **`QualiMap BamQC general alignment quality metrics report` :** A detailed HTML report containing mapping quality metrics, GC content, and coverage statistics.\n* **`mapDamage Visualisation` :** Visual plots displaying the characteristic C-to-T deamination patterns at the ends of ancient DNA reads.\n* **`Kraken2 taxonomic classification and microbial screening report` :** A tabular report showing the taxonomic classification of unmapped reads.\n* **`EndorSpy endogenous DNA authentication report` :** A JSON file containing the calculated endogenous DNA percentage.\n* **`Sex.DetERRmine (Without BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for human-genome alignments.\n* **`Sex.DetERRmine (With BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for targeted capture regions.\n* **`Mitochondrial to nuclear DNA ratio calculation report` :** A JSON file containing the calculated ratio between mitochondrial and nuclear reads.\n* **`ANGSD report of nuclear contamination estimation` :** A tabular text file detailing the estimates of nuclear X-chromosome contamination.\n* **`Bcftools variant calling summary statistics report` :** A text file containing comprehensive summary statistics for the called variants (VCF).\n* **`Fully post-processed mapping results` :** The final deduplicated and filtered alignment BAM file.\n* **`FreeBayes raw genomic variant calls` :** The raw VCF file generated from variant analysis.\n\n\n## Testing Data\nTo ensure the workflow functions correctly, it was validated using the following datasets and databases:\n\n* **`Primary Test Data` :** A downsampled paired-end FASTQ dataset [NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz) and [NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz) optimized for rapid workflow testing and validation.\n* **`Primary Reference Genome` :** The [hs37d5_chr21-MT.fa.gz](https://github.com/nf-core/test-datasets/blob/eager/reference/Human/hs37d5_chr21-MT.fa.gz) file was utilized as the primary reference genome sequence.\n* **`X-Chromosome Contamination Reference` :** The [HapMap ChrX](https://github.com/ANGSD/angsd/blob/master/RES/HapMapChrX.gz) dataset was provided as the initial reference for the estimation of X-chromosome contamination using the ANGSD tool.\n* **`Taxonomic Classification Database` :** The Minikraken v2 database was utilized to perform taxonomic classification via Kraken2.", + "readme": "# Ancient DNA analysis pipeline\nThis workflow performs an ancient DNA (aDNA) based analysis similar to the one in the [nf-core/eager](https://nf-co.re/eager/2.5.3/) workflow. nf-core/eager is a bioinformatics best-practice processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.\n\nThe pipeline processes the sequencing-read input provided to the workflow together with a reference genome and optional supporting reference data. It aligns reads and performs extensive general NGS and aDNA-specific quality control on the results.\n\n\n## Required & Optional Inputs\nTo run this workflow successfully, you need to provide the following input datasets and parameters:\n\n* **`Input FASTQ reads` :** Input FASTQ reads for the sample, as a list of paired or unpaired reads (a `list:paired_or_unpaired` collection). Each element of the list is either a pair of forward and reverse reads or a single unpaired dataset, so single-end and paired-end samples are given to the workflow the same way \u2014 and a single run may mix both. Galaxy routes each element down the appropriate trimming and mapping path automatically, so no read-type parameter is needed.\n* **`Reference genome` :** Reference genome sequence in FASTA format. This is essential for read mapping and variant calling.\n* **`Choose Mapper` :** Switch to select the alignment tool. Choose between BWA and Bowtie2.\n* **`HapMap chromosome X reference` :** Optional HapMap dataset used for X-chromosome contamination estimation in ANGSD (used only if provided).\n* **`Input Mitochondrial Chromosome Name` :** The exact header name of the mitochondrial chromosome in your reference FASTA file (e.g., MT, chrM, rCRS).\n* **`Kraken2 database directory` :** The database directory required for Kraken2 taxonomic classification.\n* **`Optional BED file for Sex.DetERRmine` :** An optional BED file containing specific genomic coordinates to restrict the Sex.DetERRmine analysis. Leave empty for standard whole-genome human analysis, or provide targeted regions to enable gender estimation for non-human organisms.\n* **`ANGSD region parameter` :** The specific genomic region to restrict the ANGSD analysis (e.g. 'X:5000000-154900000' for human male nuclear contamination estimation; adjust for your reference).\n\n\n## Workflow Steps\nBy default the pipeline currently performs the following:\n\n## 1. Preprocessing and Quality Control\n* **Quality Control:** Evaluates read quality before and after trimming (`FastQC`)\n* **Adapter Trimming:** Removes adapter sequences (`AdapterRemoval`)\n\n## 2. Read Mapping and Processing\n* **Alignment:** Maps reads to the provided reference genome conditionally using either (`BWA`) or (`Bowtie2`) based on user selection\n* **Filtering and Statistics:** Separates unmapped reads and calculates alignment statistics (`Samtools View and Flagstat`)\n* **Duplicate Removal:** Detects and marks PCR duplicates (`Picard MarkDuplicates`)\n* **Alignment Quality:** Generates detailed BAM quality metrics (`QualiMap BamQC`)\n* **Library Complexity:** Estimates library complexity (`Preseq`)\n\n## 3. Ancient DNA (aDNA) Analysis\n* **Damage Profiling:** Visualizes aDNA-specific C-to-T damage patterns (`mapDamage`)\n* **Endogenous Content:** Calculates the proportion of endogenous (target) DNA in the sample (`EndorSpy`)\n* **(`Optional`) Contamination:** Estimates nuclear X-chromosome contamination conditionally if HapMap data is provided (`ANGSD X-Contamination`)\n\n## 4. Biological Information\n* **Sex Determination:** Determines biological sex based on relative chromosome coverage ratio. This step adapts conditionally whether an optional BED file is provided (`Sex.DetERRmine`)\n* **Mt/Nuc Ratio:** Calculates the ratio of mitochondrial reads to nuclear reads utilizing the specified mitochondrial chromosome name (`MtNucRatioCalculator`)\n\n## 5. Genotyping\n* **Variant Analysis:** Performs variant calling to generate VCF files (`FreeBayes`)\n* **Variant Statistics:** Calculates statistics for the generated variants (`Bcftools stats`)\n\n## 6. Metagenomic Screening (For Unmapped Reads)\n* **Read Extraction:** Extracts unmapped reads for microbial analysis (`Picard SamToFastq`)\n* **Quality Filter:** Filters low-complexity sequences (`BBTools BBduk`)\n* **Taxonomic Classification:** Performs microbiome/taxonomic screening on the filtered unmapped reads (`Kraken2`)\n\n## 7. Reporting\n* **Summary Report:** Aggregates logs and statistics from all these tools into a single interactive HTML report (`MultiQC`)\n\n\n## Workflow Outputs\nUpon successful execution, the workflow explicitly provides the following final files for analysis:\n\n* **`MultiQC aggregated workflow summary report` :** An interactive HTML report aggregating QC and analysis logs from all tools.\n* **`QualiMap BamQC general alignment quality metrics report` :** A detailed HTML report containing mapping quality metrics, GC content, and coverage statistics.\n* **`mapDamage Visualisation` :** Visual plots displaying the characteristic C-to-T deamination patterns at the ends of ancient DNA reads.\n* **`Kraken2 taxonomic classification and microbial screening report` :** A tabular report showing the taxonomic classification of unmapped reads.\n* **`EndorSpy endogenous DNA authentication report` :** A JSON file containing the calculated endogenous DNA percentage.\n* **`Sex.DetERRmine (Without BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for human-genome alignments.\n* **`Sex.DetERRmine (With BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for targeted capture regions.\n* **`Mitochondrial to nuclear DNA ratio calculation report` :** A JSON file containing the calculated ratio between mitochondrial and nuclear reads.\n* **`ANGSD report of nuclear contamination estimation` :** A tabular text file detailing the estimates of nuclear X-chromosome contamination.\n* **`Bcftools variant calling summary statistics report` :** A text file containing comprehensive summary statistics for the called variants (VCF).\n* **`Fully post-processed mapping results` :** The final deduplicated and filtered alignment BAM file.\n* **`FreeBayes raw genomic variant calls` :** The raw VCF file generated from variant analysis.\n\n\n## Testing Data\nTo ensure the workflow functions correctly, it was validated using the following datasets and databases:\n\n* **`Primary Test Data` :** A downsampled paired-end FASTQ dataset [NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz) and [NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz) optimized for rapid workflow testing and validation.\n* **`Primary Reference Genome` :** The [hs37d5_chr21-MT.fa.gz](https://github.com/nf-core/test-datasets/blob/eager/reference/Human/hs37d5_chr21-MT.fa.gz) file was utilized as the primary reference genome sequence.\n* **`X-Chromosome Contamination Reference` :** The [HapMap ChrX](https://github.com/ANGSD/angsd/blob/master/RES/HapMapChrX.gz) dataset was provided as the initial reference for the estimation of X-chromosome contamination using the ANGSD tool.\n* **`Taxonomic Classification Database` :** The Minikraken v2 database was utilized to perform taxonomic classification via Kraken2.", + "release": "0.1", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, "steps": { "0": { - "annotation": "Input single-end FASTQ reads for the sample.", + "annotation": "Input FASTQ reads for the sample. Accepts single-end (unpaired) reads, paired-end reads, or a mix of both.", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Input single-end FASTQ reads for the sample.", - "name": "Input Single-end reads" - } - ], - "label": "Input Single-end reads", - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 2.664238753812697, - "top": 289.4272202709404 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"format\": [\"fastq.gz\", \"fastqsanger.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "f7d7cb77-f9c3-4f80-8c20-a4891e9cbde2", - "when": null, - "workflow_outputs": [] - }, - "1": { - "annotation": "Select the sequencing read type of your input data: Single-End (SE) or Paired-End (PE).", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Select the sequencing read type of your input data: Single-End (SE) or Paired-End (PE).", - "name": "Choose Read Type" - } - ], - "label": "Choose Read Type", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 2.439246020506289, - "top": 526.1635652932443 - }, - "tool_id": null, - "tool_state": "{\"multiple\": false, \"validators\": [], \"restrictions\": [\"Single-End\", \"Paired-End\"], \"parameter_type\": \"text\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "14d93c50-9e41-47c7-ae44-2370ec91b23f", - "when": null, - "workflow_outputs": [] - }, - "2": { - "annotation": "Input paired-end Forward FASTQ reads for the sample. Please ensure that the files in this collection are sorted alphabetically so they correctly match the R2/R1 files.", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "Input paired-end Forward FASTQ reads for the sample. Please ensure that the files in this collection are sorted alphabetically so they correctly match the R2/R1 files.", - "name": "Input Paired-end Forward reads (R1)" - } - ], - "label": "Input Paired-end Forward reads (R1)", - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 0.8459904296869354, - "top": 791.502398805326 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"format\": [\"fastq.gz\", \"fastqsanger.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "182acaba-5521-4972-9d17-c51a485160f9", - "when": null, - "workflow_outputs": [] - }, - "3": { - "annotation": "Input paired-end Reverse FASTQ reads for the sample. Please ensure that the files in this collection are sorted alphabetically so they correctly match the R2/R1 files.", - "content_id": null, - "errors": null, - "id": 3, - "input_connections": {}, - "inputs": [ - { - "description": "Input paired-end Reverse FASTQ reads for the sample. Please ensure that the files in this collection are sorted alphabetically so they correctly match the R2/R1 files.", - "name": "Input Paired-end reverse reads (R2)" + "description": "Input FASTQ reads for the sample. Accepts single-end (unpaired) reads, paired-end reads, or a mix of both.", + "name": "Input FASTQ reads" } ], - "label": "Input Paired-end reverse reads (R2)", + "label": "Input FASTQ reads", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 909.1024659439979 + "top": 646.0483626302844 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"format\": [\"fastq.gz\", \"fastqsanger.gz\"], \"tag\": null, \"collection_type\": \"list\", \"fields\": null, \"column_definitions\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\"], \"tag\": null, \"collection_type\": \"list:paired_or_unpaired\", \"fields\": null, \"column_definitions\": null}", "tool_version": null, "type": "data_collection_input", - "uuid": "8bc74801-26a1-4ea3-90a4-46ba6d8ee2eb", + "uuid": "2baea52a-fb64-4a35-b9a4-b877a6237e91", "when": null, "workflow_outputs": [] }, - "4": { + "1": { "annotation": "Switch to select the alignment tool.", "content_id": null, "errors": null, - "id": 4, + "id": 1, "input_connections": {}, "inputs": [ { @@ -142,22 +61,22 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 1594.510627584606, + "left": 1595.1210697204956, "top": 1441.097440599871 }, "tool_id": null, "tool_state": "{\"multiple\": false, \"validators\": [], \"restrictions\": [\"BWA\", \"Bowtie2\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "6fb6f861-a6bf-4cc7-9afd-0bbbcb8d6c6c", + "uuid": "78385aa4-e415-4b9a-a930-a89dd93ef19f", "when": null, "workflow_outputs": [] }, - "5": { + "2": { "annotation": "An optional BED file containing specific genomic coordinates to restrict the Sex.DetERRmine analysis. Leave empty for standard whole-genome human analysis, or provide targeted regions to enable gender estimation for non-human organisms.", "content_id": null, "errors": null, - "id": 5, + "id": 2, "input_connections": {}, "inputs": [ { @@ -169,22 +88,22 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 3000.721983263028, + "left": 3001.3324253989176, "top": 250.7172256717161 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "ab2309d8-46e7-4142-a5fa-f35008e090d8", + "uuid": "6a2031d0-d965-4117-b064-3787b9c06fa1", "when": null, "workflow_outputs": [] }, - "6": { + "3": { "annotation": "Reference genome sequence in FASTA format.", "content_id": null, "errors": null, - "id": 6, + "id": 3, "input_connections": {}, "inputs": [ { @@ -196,22 +115,22 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 1796.9138118486842, + "left": 1797.5242539845738, "top": 2815.7042121761183 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - 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