opencode-knowledge-work 0.0.0-stage → 0.1.1

package/content/bio-research/skills/bio-research-nextflow-development/LICENSE.txt

@@ -0,0 +1,201 @@
+Apache License
+Version 2.0, January 2004
+http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+"License" shall mean the terms and conditions for use, reproduction,
+and distribution as defined by Sections 1 through 9 of this document.
+
+"Licensor" shall mean the copyright owner or entity authorized by
+the copyright owner that is granting the License.
+
+"Legal Entity" shall mean the union of the acting entity and all
+other entities that control, are controlled by, or are under common
+control with that entity. For the purposes of this definition,
+"control" means (i) the power, direct or indirect, to cause the
+direction or management of such entity, whether by contract or
+otherwise, or (ii) ownership of fifty percent (50%) or more of the
+outstanding shares, or (iii) beneficial ownership of such entity.
+
+"You" (or "Your") shall mean an individual or Legal Entity
+exercising permissions granted by this License.
+
+"Source" form shall mean the preferred form for making modifications,
+including but not limited to software source code, documentation
+source, and configuration files.
+
+"Object" form shall mean any form resulting from mechanical
+transformation or translation of a Source form, including but
+not limited to compiled object code, generated documentation,
+and conversions to other media types.
+
+"Work" shall mean the work of authorship, whether in Source or
+Object form, made available under the License, as indicated by a
+copyright notice that is included in or attached to the work
+(an example is provided in the Appendix below).
+
+"Derivative Works" shall mean any work, whether in Source or Object
+form, that is based on (or derived from) the Work and for which the
+editorial revisions, annotations, elaborations, or other modifications
+represent, as a whole, an original work of authorship. For the purposes
+of this License, Derivative Works shall not include works that remain
+separable from, or merely link (or bind by name) to the interfaces of,
+the Work and Derivative Works thereof.
+
+"Contribution" shall mean any work of authorship, including
+the original version of the Work and any modifications or additions
+to that Work or Derivative Works thereof, that is intentionally
+submitted to Licensor for inclusion in the Work by the copyright owner
+or by an individual or Legal Entity authorized to submit on behalf of
+the copyright owner. For the purposes of this definition, "submitted"
+means any form of electronic, verbal, or written communication sent
+to the Licensor or its representatives, including but not limited to
+communication on electronic mailing lists, source code control systems,
+and issue tracking systems that are managed by, or on behalf of, the
+Licensor for the purpose of discussing and improving the Work, but
+excluding communication that is conspicuously marked or otherwise
+designated in writing by the copyright owner as "Not a Contribution."
+
+"Contributor" shall mean Licensor and any individual or Legal Entity
+on behalf of whom a Contribution has been received by Licensor and
+subsequently incorporated within the Work.
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+copyright license to reproduce, prepare Derivative Works of,
+publicly display, publicly perform, sublicense, and distribute the
+Work and such Derivative Works in Source or Object form.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+(except as stated in this section) patent license to make, have made,
+use, offer to sell, sell, import, and otherwise transfer the Work,
+where such license applies only to those patent claims licensable
+by such Contributor that are necessarily infringed by their
+Contribution(s) alone or by combination of their Contribution(s)
+with the Work to which such Contribution(s) was submitted. If You
+institute patent litigation against any entity (including a
+cross-claim or counterclaim in a lawsuit) alleging that the Work
+or a Contribution incorporated within the Work constitutes direct
+or contributory patent infringement, then any patent licenses
+granted to You under this License for that Work shall terminate
+as of the date such litigation is filed.
+
+4. Redistribution. You may reproduce and distribute copies of the
+Work or Derivative Works thereof in any medium, with or without
+modifications, and in Source or Object form, provided that You
+meet the following conditions:
+
+(a) You must give any other recipients of the Work or
+Derivative Works a copy of this License; and
+
+(b) You must cause any modified files to carry prominent notices
+stating that You changed the files; and
+
+(c) You must retain, in the Source form of any Derivative Works
+that You distribute, all copyright, patent, trademark, and
+attribution notices from the Source form of the Work,
+excluding those notices that do not pertain to any part of
+the Derivative Works; and
+
+(d) If the Work includes a "NOTICE" text file as part of its
+distribution, then any Derivative Works that You distribute must
+include a readable copy of the attribution notices contained
+within such NOTICE file, excluding those notices that do not
+pertain to any part of the Derivative Works, in at least one
+of the following places: within a NOTICE text file distributed
+as part of the Derivative Works; within the Source form or
+documentation, if provided along with the Derivative Works; or,
+within a display generated by the Derivative Works, if and
+wherever such third-party notices normally appear. The contents
+of the NOTICE file are for informational purposes only and
+do not modify the License. You may add Your own attribution
+notices within Derivative Works that You distribute, alongside
+or as an addendum to the NOTICE text from the Work, provided
+that such additional attribution notices cannot be construed
+as modifying the License.
+
+You may add Your own copyright statement to Your modifications and
+may provide additional or different license terms and conditions
+for use, reproduction, or distribution of Your modifications, or
+for any such Derivative Works as a whole, provided Your use,
+reproduction, and distribution of the Work otherwise complies with
+the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+any Contribution intentionally submitted for inclusion in the Work
+by You to the Licensor shall be under the terms and conditions of
+this License, without any additional terms or conditions.
+Notwithstanding the above, nothing herein shall supersede or modify
+the terms of any separate license agreement you may have executed
+with Licensor regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+names, trademarks, service marks, or product names of the Licensor,
+except as required for reasonable and customary use in describing the
+origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or
+agreed to in writing, Licensor provides the Work (and each
+Contributor provides its Contributions) on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+implied, including, without limitation, any warranties or conditions
+of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+PARTICULAR PURPOSE. You are solely responsible for determining the
+appropriateness of using or redistributing the Work and assume any
+risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+whether in tort (including negligence), contract, or otherwise,
+unless required by applicable law (such as deliberate and grossly
+negligent acts) or agreed to in writing, shall any Contributor be
+liable to You for damages, including any direct, indirect, special,
+incidental, or consequential damages of any character arising as a
+result of this License or out of the use or inability to use the
+Work (including but not limited to damages for loss of goodwill,
+work stoppage, computer failure or malfunction, or any and all
+other commercial damages or losses), even if such Contributor
+has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+the Work or Derivative Works thereof, You may choose to offer,
+and charge a fee for, acceptance of support, warranty, indemnity,
+or other liability obligations and/or rights consistent with this
+License. However, in accepting such obligations, You may act only
+on Your own behalf and on Your sole responsibility, not on behalf
+of any other Contributor, and only if You agree to indemnify,
+defend, and hold each Contributor harmless for any liability
+incurred by, or claims asserted against, such Contributor by reason
+of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+To apply the Apache License to your work, attach the following
+boilerplate notice, with the fields enclosed by brackets "[]"
+replaced with your own identifying information. (Don't include
+the brackets!) The text should be enclosed in the appropriate
+comment syntax for the file format. We also recommend that a
+file or class name and description of purpose be included on the
+same "printed page" as the copyright notice for easier
+identification within third-party archives.
+
+Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

package/content/bio-research/skills/bio-research-nextflow-development/SKILL.md

@@ -0,0 +1,290 @@
+---
+name: nextflow-development
+description: Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
+---
+
+# nf-core Pipeline Deployment
+
+Run nf-core bioinformatics pipelines on local or public sequencing data.
+
+**Target users:** Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis.
+
+## Workflow Checklist
+
+```
+- [ ] Step 0: Acquire data (if from GEO/SRA)
+- [ ] Step 1: Environment check (MUST pass)
+- [ ] Step 2: Select pipeline (confirm with user)
+- [ ] Step 3: Run test profile (MUST pass)
+- [ ] Step 4: Create samplesheet
+- [ ] Step 5: Configure & run (confirm genome with user)
+- [ ] Step 6: Verify outputs
+```
+
+---
+
+## Step 0: Acquire Data (GEO/SRA Only)
+
+**Skip this step if user has local FASTQ files.**
+
+For public datasets, fetch from GEO/SRA first. See [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) for the full workflow.
+
+**Quick start:**
+
+```bash
+# 1. Get study info
+python scripts/sra_geo_fetch.py info GSE110004
+
+# 2. Download (interactive mode)
+python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i
+
+# 3. Generate samplesheet
+python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv
+```
+
+**DECISION POINT:** After fetching study info, confirm with user:
+- Which sample subset to download (if multiple data types)
+- Suggested genome and pipeline
+
+Then continue to Step 1.
+
+---
+
+## Step 1: Environment Check
+
+**Run first. Pipeline will fail without passing environment.**
+
+```bash
+python scripts/check_environment.py
+```
+
+All critical checks must pass. If any fail, provide fix instructions:
+
+### Docker issues
+
+| Problem | Fix |
+|---------|-----|
+| Not installed | Install from https://docs.docker.com/get-docker/ |
+| Permission denied | `sudo usermod -aG docker $USER` then re-login |
+| Daemon not running | `sudo systemctl start docker` |
+
+### Nextflow issues
+
+| Problem | Fix |
+|---------|-----|
+| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
+| Version < 23.04 | `nextflow self-update` |
+
+### Java issues
+
+| Problem | Fix |
+|---------|-----|
+| Not installed / < 11 | `sudo apt install openjdk-11-jdk` |
+
+**Do not proceed until all checks pass.** For HPC/Singularity, see [references/troubleshooting.md](references/troubleshooting.md).
+
+---
+
+## Step 2: Select Pipeline
+
+**DECISION POINT: Confirm with user before proceeding.**
+
+| Data Type | Pipeline | Version | Goal |
+|-----------|----------|---------|------|
+| RNA-seq | `rnaseq` | 3.22.2 | Gene expression |
+| WGS/WES | `sarek` | 3.7.1 | Variant calling |
+| ATAC-seq | `atacseq` | 2.1.2 | Chromatin accessibility |
+
+Auto-detect from data:
+```bash
+python scripts/detect_data_type.py /path/to/data
+```
+
+For pipeline-specific details:
+- [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md)
+- [references/pipelines/sarek.md](references/pipelines/sarek.md)
+- [references/pipelines/atacseq.md](references/pipelines/atacseq.md)
+
+---
+
+## Step 3: Run Test Profile
+
+**Validates environment with small data. MUST pass before real data.**
+
+```bash
+nextflow run nf-core/<pipeline> -r <version> -profile test,docker --outdir test_output
+```
+
+| Pipeline | Command |
+|----------|---------|
+| rnaseq | `nextflow run nf-core/rnaseq -r 3.22.2 -profile test,docker --outdir test_rnaseq` |
+| sarek | `nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek` |
+| atacseq | `nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq` |
+
+Verify:
+```bash
+ls test_output/multiqc/multiqc_report.html
+grep "Pipeline completed successfully" .nextflow.log
+```
+
+If test fails, see [references/troubleshooting.md](references/troubleshooting.md).
+
+---
+
+## Step 4: Create Samplesheet
+
+### Generate automatically
+
+```bash
+python scripts/generate_samplesheet.py /path/to/data <pipeline> -o samplesheet.csv
+```
+
+The script:
+- Discovers FASTQ/BAM/CRAM files
+- Pairs R1/R2 reads
+- Infers sample metadata
+- Validates before writing
+
+**For sarek:** Script prompts for tumor/normal status if not auto-detected.
+
+### Validate existing samplesheet
+
+```bash
+python scripts/generate_samplesheet.py --validate samplesheet.csv <pipeline>
+```
+
+### Samplesheet formats
+
+**rnaseq:**
+```csv
+sample,fastq_1,fastq_2,strandedness
+SAMPLE1,/abs/path/R1.fq.gz,/abs/path/R2.fq.gz,auto
+```
+
+**sarek:**
+```csv
+patient,sample,lane,fastq_1,fastq_2,status
+patient1,tumor,L001,/abs/path/tumor_R1.fq.gz,/abs/path/tumor_R2.fq.gz,1
+patient1,normal,L001,/abs/path/normal_R1.fq.gz,/abs/path/normal_R2.fq.gz,0
+```
+
+**atacseq:**
+```csv
+sample,fastq_1,fastq_2,replicate
+CONTROL,/abs/path/ctrl_R1.fq.gz,/abs/path/ctrl_R2.fq.gz,1
+```
+
+---
+
+## Step 5: Configure & Run
+
+### 5a. Check genome availability
+
+```bash
+python scripts/manage_genomes.py check <genome>
+# If not installed:
+python scripts/manage_genomes.py download <genome>
+```
+
+Common genomes: GRCh38 (human), GRCh37 (legacy), GRCm39 (mouse), R64-1-1 (yeast), BDGP6 (fly)
+
+### 5b. Decision points
+
+**DECISION POINT: Confirm with user:**
+
+1. **Genome:** Which reference to use
+2. **Pipeline-specific options:**
+   - **rnaseq:** aligner (star_salmon recommended, hisat2 for low memory)
+   - **sarek:** tools (haplotypecaller for germline, mutect2 for somatic)
+   - **atacseq:** read_length (50, 75, 100, or 150)
+
+### 5c. Run pipeline
+
+```bash
+nextflow run nf-core/<pipeline> \
+    -r <version> \
+    -profile docker \
+    --input samplesheet.csv \
+    --outdir results \
+    --genome <genome> \
+    -resume
+```
+
+**Key flags:**
+- `-r`: Pin version
+- `-profile docker`: Use Docker (or `singularity` for HPC)
+- `--genome`: iGenomes key
+- `-resume`: Continue from checkpoint
+
+**Resource limits (if needed):**
+```bash
+--max_cpus 8 --max_memory '32.GB' --max_time '24.h'
+```
+
+---
+
+## Step 6: Verify Outputs
+
+### Check completion
+
+```bash
+ls results/multiqc/multiqc_report.html
+grep "Pipeline completed successfully" .nextflow.log
+```
+
+### Key outputs by pipeline
+
+**rnaseq:**
+- `results/star_salmon/salmon.merged.gene_counts.tsv` - Gene counts
+- `results/star_salmon/salmon.merged.gene_tpm.tsv` - TPM values
+
+**sarek:**
+- `results/variant_calling/*/` - VCF files
+- `results/preprocessing/recalibrated/` - BAM files
+
+**atacseq:**
+- `results/macs2/narrowPeak/` - Peak calls
+- `results/bwa/mergedLibrary/bigwig/` - Coverage tracks
+
+---
+
+## Quick Reference
+
+For common exit codes and fixes, see [references/troubleshooting.md](references/troubleshooting.md).
+
+### Resume failed run
+
+```bash
+nextflow run nf-core/<pipeline> -resume
+```
+
+---
+
+## References
+
+- [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) - Downloading public GEO/SRA data
+- [references/troubleshooting.md](references/troubleshooting.md) - Common issues and fixes
+- [references/installation.md](references/installation.md) - Environment setup
+- [references/pipelines/rnaseq.md](references/pipelines/rnaseq.md) - RNA-seq pipeline details
+- [references/pipelines/sarek.md](references/pipelines/sarek.md) - Variant calling details
+- [references/pipelines/atacseq.md](references/pipelines/atacseq.md) - ATAC-seq details
+
+---
+
+## Disclaimer
+
+This skill is provided as a prototype example demonstrating how to integrate nf-core bioinformatics pipelines into Claude Code for automated analysis workflows. The current implementation supports three pipelines (rnaseq, sarek, and atacseq), serving as a foundation that enables the community to expand support to the full set of nf-core pipelines.
+
+It is intended for educational and research purposes and should not be considered production-ready without appropriate validation for your specific use case. Users are responsible for ensuring their computing environment meets pipeline requirements and for verifying analysis results.
+
+Anthropic does not guarantee the accuracy of bioinformatics outputs, and users should follow standard practices for validating computational analyses. This integration is not officially endorsed by or affiliated with the nf-core community.
+
+## Attribution
+
+When publishing results, cite the appropriate pipeline. Citations are available in each nf-core repository's CITATIONS.md file (e.g., https://github.com/nf-core/rnaseq/blob/3.22.2/CITATIONS.md).
+
+## Licenses
+
+- **nf-core pipelines:** MIT License (https://nf-co.re/about)
+- **Nextflow:** Apache License, Version 2.0 (https://www.nextflow.io/about-us.html)
+- **NCBI SRA Toolkit:** Public Domain (https://github.com/ncbi/sra-tools/blob/master/LICENSE)