pathogen-repo-build: Move build.log outside of working directory

The entire working directory gets zipped and uploaded to AWS Batch when
using the `aws-batch` runtime, which includes an early `build.log` file.
When the build completes and downloads the build outputs, the early
`build.log` file overwrites the local `build.log` of the GH Action.
This results in a truncated file that does not include the
AWS_BATCH_JOB_ID and prevents the generation of the AWS Batch summary.

This commit moves the hard-coded `build.log` file to outside of the
current working directory to prevent it from being uploaded with the
pathogen repo build.

.github/workflows/pathogen-repo-build.yaml

@@ -98,14 +98,14 @@ on:
           The default paths included in the artifact are:
 
 
-            build.log
+            ../build.log
             auspice/
             results/
             benchmarks/
             logs/
             .snakemake/log/
 
-          The "build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
+          The "../build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
 
           This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
         type: string
@@ -189,14 +189,14 @@ on:
           The default paths included in the artifact are:
 
 
-            build.log
+            ../build.log
             auspice/
             results/
             benchmarks/
             logs/
             .snakemake/log/
 
-          The "build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
+          The "../build.log" contains log messages from the `nextstrain build` command. The other paths are common output paths for Nextstrain builds. If a path does not exist in your build, then the action will still succeed and will print out a warning for the non-existent file(s). Use an exclude pattern for any of the default paths that you would like to exclude from the artifact (e.g. !build.log).
 
           This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
         type: string
@@ -274,14 +274,14 @@ jobs:
           # shellcheck disable=SC2154
           set -x
 
-          eval "$NEXTSTRAIN_BUILD_COMMAND" |& tee build.log
+          eval "$NEXTSTRAIN_BUILD_COMMAND" |& tee ../build.log
       # Attempt to get the AWS Batch ID even if the run build command failed
-      # as long as the runtime is `aws-batch` and the `build.log` file exists
-      - if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('build.log') != '' }}
+      # as long as the runtime is `aws-batch` and the `../build.log` file exists
+      - if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('../build.log') != '' }}
         name: Get AWS Batch job id
         id: aws-batch
         run: |
-          echo "AWS_BATCH_JOB_ID=$(sed -nE 's/.+AWS Batch Job ID\:.+ ([-a-f0-9]+)$/\1/p' < build.log)" | tee -a "$GITHUB_ENV"
+          echo "AWS_BATCH_JOB_ID=$(sed -nE 's/.+AWS Batch Job ID\:.+ ([-a-f0-9]+)$/\1/p' < ../build.log)" | tee -a "$GITHUB_ENV"
       - if: ${{ always() && env.AWS_BATCH_JOB_ID }}
         name: Generate AWS Batch summary
         run: |
@@ -293,7 +293,7 @@ jobs:
           if-no-files-found: warn
           name: ${{ inputs.artifact-name }}
           path: |
-            build.log
+            ../build.log
             auspice/
             results/
             benchmarks/

.github/workflows/pathogen-repo-build.yaml.in

@@ -128,14 +128,14 @@ on:
 
           The default paths included in the artifact are:
 
-            build.log
+            ../build.log
             auspice/
             results/
             benchmarks/
             logs/
             .snakemake/log/
 
-          The "build.log" contains log messages from the `nextstrain build` command.
+          The "../build.log" contains log messages from the `nextstrain build` command.
           The other paths are common output paths for Nextstrain builds.
           If a path does not exist in your build, then the action will still
           succeed and will print out a warning for the non-existent file(s).
@@ -240,15 +240,15 @@ jobs:
           # shellcheck disable=SC2154
           set -x
 
-          eval "$NEXTSTRAIN_BUILD_COMMAND" |& tee build.log
+          eval "$NEXTSTRAIN_BUILD_COMMAND" |& tee ../build.log
 
       # Attempt to get the AWS Batch ID even if the run build command failed
-      # as long as the runtime is `aws-batch` and the `build.log` file exists
-      - if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('build.log') != '' }}
+      # as long as the runtime is `aws-batch` and the `../build.log` file exists
+      - if: ${{ always() && inputs.runtime == 'aws-batch' && hashFiles('../build.log') != '' }}
         name: Get AWS Batch job id
         id: aws-batch
         run: |
-          echo "AWS_BATCH_JOB_ID=$(sed -nE 's/.+AWS Batch Job ID\:.+ ([-a-f0-9]+)$/\1/p' < build.log)" | tee -a "$GITHUB_ENV"
+          echo "AWS_BATCH_JOB_ID=$(sed -nE 's/.+AWS Batch Job ID\:.+ ([-a-f0-9]+)$/\1/p' < ../build.log)" | tee -a "$GITHUB_ENV"
 
       - if: ${{ always() && env.AWS_BATCH_JOB_ID }}
         name: Generate AWS Batch summary
@@ -262,7 +262,7 @@ jobs:
           if-no-files-found: warn
           name: ${{ inputs.artifact-name }}
           path: |
-            build.log
+            ../build.log
             auspice/
             results/
             benchmarks/