wgcna-power-threshold

!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:

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:

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:

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

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:

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:

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

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
• technologyType = RNASeq (Steps 5) or Microarray (Step 6)

Derive inputSuffixMM:

• RNASeq: [module - membership - <strandType> - tpm - unique]
• Microarray: [module - membership - microarray]

Create the dataset output directory, copy the rsynced analysisConfig.xml and the plot into it, then insert the <step> block as a new child element immediately before the last closing tag in analysisConfig.xml:

mkdir -p ~/wgcna/$ARGUMENTS
cp /tmp/$ARGUMENTS/analysisConfig.xml ~/wgcna/$ARGUMENTS/analysisConfig.xml
cp /tmp/$ARGUMENTS/power_threshold_plot.pdf ~/wgcna/$ARGUMENTS/
cp /tmp/$ARGUMENTS/paths.txt ~/wgcna/$ARGUMENTS/paths.txt

python3 - <<'PYEOF'
import os

path = os.path.expanduser("~/wgcna/$ARGUMENTS/analysisConfig.xml")
with open(path) as f:
    content = f.read()

step_xml = """
<!-- datasetName: $ARGUMENTS | project: <projectName> | organism: <organismAbbrev> | softThresholdPower: <softThresholdPower> -->
<step class="ApiCommonData::Load::IterativeWGCNAResults">
  <property name="profileSetName" value="WGCNA $ARGUMENTS" />
  <property name="inputFile" value="<inputFileBasename>" />
  <property name="softThresholdPower" value="<softThresholdPower>" />
  <property name="organismAbbrev" value="<organismAbbrev>" />
  <property name="inputSuffixMM" value="<inputSuffixMM>" />
  <property name="technologyType" value="<technologyType>" />
  <property name="threshold" value="1" />
  <property name="samples" isReference="1" value="$globalReferencable->{samples}" />
</step>
"""

last_close = content.rfind('</')
if last_close == -1:
    content = content + step_xml
else:
    content = content[:last_close] + step_xml + content[last_close:]

with open(path, 'w') as f:
    f.write(content)

print("Step inserted into", path)
PYEOF

Report the output directory (~/wgcna/$ARGUMENTS/) and its contents to the user:

• analysisConfig.xml — rsynced file with the step XML inserted
• power_threshold_plot.pdf — scale-free topology plot used to choose the power threshold
• paths.txt — remote paths found during this run (input file and analysisConfig)