add log file name to error panel

pdimens · Aug 5, 2024 · fcb51b6 · fcb51b6
1 parent fb7670c
commit fcb51b6
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Showing 22 changed files with 22 additions and 22 deletions.
diff --git a/src/harpy/printfunctions.py b/src/harpy/printfunctions.py
@@ -8,7 +8,7 @@
 def print_onstart(text, title):
     """Print a panel of info on workflow run"""
     print("")
-    print(Panel(text, title = f"[bold]Harpy {title}", title_align = "left", border_style = "light_steel_blue", subtitle = "Running Workflow", width = 75), file = sys.stderr)
+    print(Panel(text, title = f"[bold]harpy {title}", title_align = "left", border_style = "light_steel_blue", subtitle = "Running Workflow", width = 75), file = sys.stderr)
 
 def print_error(errortext):
     """Print a yellow panel with error text"""

diff --git a/src/harpy/snakefiles/align_bwa.smk b/src/harpy/snakefiles/align_bwa.smk
@@ -31,7 +31,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy align bwa",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/align_ema.smk b/src/harpy/snakefiles/align_ema.smk
@@ -35,7 +35,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy align ema",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/align_strobealign.smk b/src/harpy/snakefiles/align_strobealign.smk
@@ -33,7 +33,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy align strobealign",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/deconvolve.smk b/src/harpy/snakefiles/deconvolve.smk
@@ -43,7 +43,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy deconvolve",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/demultiplex_gen1.smk b/src/harpy/snakefiles/demultiplex_gen1.smk
@@ -40,7 +40,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy demultiplex",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/impute.smk b/src/harpy/snakefiles/impute.smk
@@ -40,7 +40,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            "The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy impute",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/phase.smk b/src/harpy/snakefiles/phase.smk
@@ -67,7 +67,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy phase",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/preflight_bam.smk b/src/harpy/snakefiles/preflight_bam.smk
@@ -27,7 +27,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy preflight bam",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/preflight_fastq.smk b/src/harpy/snakefiles/preflight_fastq.smk
@@ -27,7 +27,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy preflight fastq",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/qc.smk b/src/harpy/snakefiles/qc.smk
@@ -52,7 +52,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy qc",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/simulate_linkedreads.smk b/src/harpy/snakefiles/simulate_linkedreads.smk
@@ -43,7 +43,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy simulate reads",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/simulate_snpindel.smk b/src/harpy/snakefiles/simulate_snpindel.smk
@@ -81,7 +81,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy simulate snpindel",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/simulate_variants.smk b/src/harpy/snakefiles/simulate_variants.smk
@@ -68,7 +68,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = f"[bold]harpy simulate {variant}",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/snp_freebayes.smk b/src/harpy/snakefiles/snp_freebayes.smk
@@ -54,7 +54,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy snp freebayes",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/snp_mpileup.smk b/src/harpy/snakefiles/snp_mpileup.smk
@@ -49,7 +49,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy snp mpileup",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_leviathan.smk b/src/harpy/snakefiles/sv_leviathan.smk
@@ -36,7 +36,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv leviathan",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_leviathan_pop.smk b/src/harpy/snakefiles/sv_leviathan_pop.smk
@@ -34,7 +34,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv leviathan",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_naibr.smk b/src/harpy/snakefiles/sv_naibr.smk
@@ -49,7 +49,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv naibr",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_naibr_phase.smk b/src/harpy/snakefiles/sv_naibr_phase.smk
@@ -43,7 +43,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv naibr",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_naibr_pop.smk b/src/harpy/snakefiles/sv_naibr_pop.smk
@@ -36,7 +36,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv naibr",
             title_align = "left",
             border_style = "red"

diff --git a/src/harpy/snakefiles/sv_naibr_pop_phase.smk b/src/harpy/snakefiles/sv_naibr_pop_phase.smk
@@ -40,7 +40,7 @@ onerror:
     print("")
     rprint(
         Panel(
-            f"The workflow has terminated due to an error. See the log file below for more details.",
+            f"The workflow has terminated due to an error. See the log file for more details:\n[bold]{outdir}/logs/snakemake/{dt_string}.snakelog[/bold]",
             title = "[bold]harpy sv naibr",
             title_align = "left",
             border_style = "red"