diff --git a/src/harpy/printfunctions.py b/src/harpy/printfunctions.py index b96bae925..aa34181ab 100644 --- 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 index 093f9c09f..1e506e342 100644 --- 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 index 46378984c..3138c06b8 100644 --- 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 index ec944e7c1..4f3bc92c1 100644 --- 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 index 80295ccae..2d7d26e7f 100644 --- 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 index 26795cac4..5c4b12da3 100644 --- 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 index 7b0d28bec..1db6eef8c 100644 --- 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 index d2b0bf637..df2387b74 100644 --- 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 index 08d2c3884..f07f7d778 100644 --- 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 index 7beb12b73..6c2d5efb3 100644 --- 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 index 77ff85a9d..c9b56cfd4 100644 --- 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 index 26c95a9ba..76b26def1 100644 --- 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 index a065c7374..b60e11a4a 100644 --- 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 index 5eed5f50e..348453964 100644 --- 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 index a32b21098..3de06f040 100644 --- 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 index 18e2f9574..75bef02e0 100644 --- 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 index 599ab09e8..5d7189d18 100644 --- 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 index 170892eab..d1d0ae587 100644 --- 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 index c21069bd0..c79e94f70 100644 --- 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 index bb109810a..4eb29b53d 100644 --- 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 index dddeeb924..a99d4c055 100644 --- 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 index 2634ac833..37acf43dd 100644 --- 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"