trees_gene_groups/gene_groups-COPYME STEP_3: fix newick-existence false-skip

gene_groups-COPYME's STEP_3 orchestrator was using

    ls "${NEWICK_DIR}"/*.fasttree "${NEWICK_DIR}"/*.treefile \
       "${NEWICK_DIR}"/*.veryfasttree "${NEWICK_DIR}"/*.phylobayes.nwk

to test "did STEP_2 produce ANY tree file for this gene group?" — but `ls`
returns exit-2 whenever ANY of the four patterns misses, so a gene group
that legitimately produced only one tree type (e.g. fasttree-only runs from
STEP_2 profile=standard) was silently skipped as "no STEP_2 newicks".

Manifested today as: STEP_3 RUN_1 in gene_groups-hugo_hgnc reported
"Setup: 0 new, 2060 skipped (no STEP_2 newicks)" even though gene_group-
synaptotagmins/ contained a valid .fasttree file at the resolved
STEP2_RUN_DIR path. The check is now:

    shopt -s nullglob
    NEWICK_FILES=( "${NEWICK_DIR}"/*.fasttree ... )
    shopt -u nullglob
    (( ${#NEWICK_FILES[@]} == 0 )) && skip

nullglob makes absent patterns expand to nothing; the array union answers
"did anything match across the four extensions". Matches the working
version already in gene_groups_hgnc-COPYME/STEP_3-*/RUN-workflow.sh.
Verified end-to-end by re-running STEP_3 RUN_1 (3 trees) + RUN_2 (1 tree,
2682 tips) in gene_groups-hugo_hgnc — all 4 trees rendered to PDF + SVG.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: 000specific

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/RUN-workflow.sh

@@ -233,9 +233,27 @@ while IFS=$'\t' read -r gene_group_id gene_group_name sanitized_name rgs_filenam
         fi
     fi
 
-    # STEP_2 must have produced at least one newick for this gene group
+    # STEP_2 must have produced at least one newick for this gene group.
+    # Uses shopt -s nullglob + array union so that an ABSENT extension produces
+    # no glob entry (rather than the literal pattern string), and `((${#arr[@]}))`
+    # tests the union for "did anything match". Prior `ls ... &>/dev/null` form
+    # returned exit-2 whenever ANY of the 4 patterns missed — false-skipping
+    # gene groups that legitimately produced just one tree type (e.g.,
+    # fasttree-only runs from STEP_2's profile=standard).
     NEWICK_DIR="${STEP2_RUN_DIR}/gene_group-${sanitized_name}"
-    if [ ! -d "${NEWICK_DIR}" ] || ! ls "${NEWICK_DIR}"/*.fasttree "${NEWICK_DIR}"/*.treefile "${NEWICK_DIR}"/*.veryfasttree "${NEWICK_DIR}"/*.phylobayes.nwk &>/dev/null; then
+    if [ ! -d "${NEWICK_DIR}" ]; then
+        no_trees_count=$((no_trees_count + 1))
+        continue
+    fi
+    shopt -s nullglob
+    NEWICK_FILES=(
+        "${NEWICK_DIR}"/*.fasttree
+        "${NEWICK_DIR}"/*.treefile
+        "${NEWICK_DIR}"/*.veryfasttree
+        "${NEWICK_DIR}"/*.phylobayes.nwk
+    )
+    shopt -u nullglob
+    if (( ${#NEWICK_FILES[@]} == 0 )); then
         no_trees_count=$((no_trees_count + 1))
         continue
     fi