wgcna-power-threshold

Files (1)

• SKILL.md

SKILL.md (first lines)

!`cat ${CLAUDE_SKILL_DIR}/../../shared/sync-dataset-steps.md`

Substitute every occurrence of `DATASET_NAME` above with: **$ARGUMENTS**

After completing the steps above you have `remotePath` — the full path to the dataset directory on yew. Continue:

---

## Step 4 — Determine data type from the remote path

Inspect `remotePath` for "rnaseq" or "microarray" (case-insensitive).

- If it contains **rnaseq** → proceed to Step 5.
- If it contains **microarray** → skip to Step 6.
- If neither is clear, stop and ask the user to clarify the data type.

---

## Step 5 — RNAseq: find the expression matrix

Search for WGCNA input files under `remotePath`:

```bash
ssh yew "find <remotePath> -type f -name 'wgcnaInput*.txt'"
```

**Case A — only `wgcnaInput_unstranded.txt` found:**
Capture its full path as `remoteInputFile`. Skip to Step 7.

**Case B — both `wgcnaInput_firststrand.txt` and `wgcnaInput_secondstrand.txt` found:**
Rsync both files locally to decide which is sense:

```bash
mkdir -p /tmp/$ARGUMENTS
rsync -aL yew:<path/to/wgcnaInput_firststrand.txt> /tmp/$ARGUMENTS/
rsync -aL yew:<path/to/wgcnaInput_secondstrand.txt> /tmp/$ARGUMENTS/
```

Run R to compare column means:

```bash
Rscript ${CLAUDE_SKILL_DIR}/../../bin/select-strand.R $ARGUMENTS
```

- If output is `AMBIGUOUS`, stop and tell the user the strand could not be determined (report both means).
- Otherwise set `remoteInputFile` to the remote path of the selected strand file. Skip to Step 7.

**Case C — no `wgcnaInput*.txt` files found:**
Stop and tell the user no WGCNA input files were found under `remotePath`.

---

## Step 6 — Microarray: find the expression matrix

```bash
ssh yew "find <remotePath> -type f -name 'profiles.txt'"
```

If exactly one file is found, capture it as `remoteInputFile`. Continue to Step 7.  
If zero files are found, stop and tell the user no `profiles.txt` was found — list all `.txt` files under `remotePath` and ask the user to pick one.  
If more than one is found, show the list and ask the user to pick one.

---

## Step 7 — Locate analysisConfig.xml via manual delivery path

!`cat ${CLAUDE_SKILL_DIR}/../../shared/manual-delivery-path.md`

Substitute every occurrence of `DATASET_NAME` above with: **$ARGUMENTS**

`technologyType` was determined in Step 4 (`RNASeq` or `Microarray`).

After completing the steps above you have `manualDeliveryPath`. The `analysisConfig.xml` lives at:

```
<manualDeliveryPath>/analysisConfig.xml
```

Rsync it along with the chosen input file:

```bash
mkdir -p /tmp/$ARGUMENTS
rsync -aL yew:<remoteInputFile> /tmp/$ARGUMENTS/
rsync -aL yew:<manualDeliveryPath>/analysisConfig.xml /tmp/$ARGUMENTS/
```

If `analysisConfig.xml` is not found on the remote (rsync exits non-zero or the file is absent), stop and tell the user it was not found at `<manualDeliveryPath>/analysisConfig.xml`.

Write a `paths.txt` file recording the key remote paths found during this run:

```bash
cat > /tmp/$ARGUMENTS/paths.txt <<EOF
datasetName:         $ARGUMENTS
remoteInputFile:     <remoteInputFile>
manualDeliveryPath:  <manualDeliveryPath>
analysisConfig:      <manualDeliveryPath>/analysisConfig.xml
EOF
```

---

## Step 8 — Determine WGCNA soft-threshold power and save plot

```bash
Rscript ${CLAUDE_SKILL_DIR}/../../bin/wgcna-power-threshold.R $ARGUMENTS
```

Capture the recommended power as `softThresholdPower`. If it is `NA`, stop and tell the user no clear threshold was found and show the fit table.

---

## Step 9 — Write per-dataset output directory

By this point you have captured:
- `datasetName` = `$ARGUMENTS`
- `softThresholdPower` from Step 8
- `organismAbbrev` from Step 2
- `inputFileBasename` = basename of `remoteInputFile`
- `strandType` = one of: `firststrand`, `secondstrand`, `unstranded`, or `microarray`

From VEuPathDB/dataset-cleaner, Apache-2.0.

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